Sickle cell disease (SCD) is one of the most common monogenic diseases in humans with multiple phenotypic expressions that can manifest as both acute and chronic complications. Although described more than a century ago, challenges in comprehensive disease management and collaborative research on this disease are compounded by the complex molecular and clinical phenotypes of SCD, environmental and psychosocial factors, limited therapeutic options and ambiguous terminology. This ambiguous terminology has hampered the integration and interoperability of existing SCD knowledge, and SCD research translation. The SCD Ontology (SCDO), which is a community-driven integrative and universal knowledge representation system for SCD, overcomes this issue by providing a controlled vocabulary developed by a group of experts in both SCD and ontology design. SCDO is the first and most comprehensive standardized human- and machine-readable resource that unambiguously represents terminology and concepts about SCD for researchers, patients and clinicians. It is built around the central concept ‘hemoglobinopathy’, allowing inclusion of non-SCD haemoglobinopathies, such as thalassaemias, which may interfere with or influence SCD phenotypic manifestations. This collaboratively developed ontology constitutes a comprehensive knowledge management system and standardized terminology of various SCD-related factors. The SCDO will promote interoperability of different research datasets, facilitate seamless data sharing and collaborations, including meta-analyses within the SCD community, and support the development and curation of data-basing and clinical informatics in SCD. Anyone can access the resource. Manually, based on terms in existing ontologies and in collaboration with sickle cell disease (SCD) experts where necessary. As necessary. Not currently following a fixed frequency. Terms/classes are added as they are identified as necessary by the sickle cell disease (SCD) community. Researchers in Hemoglobinopathy and/or sickle cell disease (SCD), SCD patients and clinicians. First draft was made available in BioPortal in May 2017 OBO Foundry standards. The field of sickle cell disease (SCD) research and care. April 2021 English GPL-3.0 The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. no definition For external terms/classes, the ontology from which the term was imported. no metadata complete - requires restrictions and relationships IAO:0000412 imported from Use on obsolete terms, relating the term to another term that can be used as a substitute. IAO:0100001 term replaced by An administrative note of use for a curator but of no use for a user. no organizational term IAO:0000232 editor_notes curator note A source from where the formal description was derived. This can be in the form of a link to a relevant webpage, the IRI of a term in an existing ontology, a reference to specific literature, etc. yes metadata complete - requires restrictions and relationships IAO:0000119 definition source description source An assertion of whether or not the term/class description is an adaptation of the description in the description source. Requested inclusion of this property into RO. Check details here again after inclusion. metadata complete - requires restrictions and relationships SCDO 'yes' indicates that only the description has been adaptation from the source. 'no' indicates that neither the label nor the description have been adapted from the source. 'only label adapted' indicates that only the label has been adapted from the source but the description is the same as that provided by the source. 'label and description adapted' indicates that both the label and the description have been adapted from the source. This property is required unless dc:creator is "SCDO". description adapted from source A relation between a disease and the age, developmental stage, or period of life at which the disease or the initial symptoms or manifestations of the disease usually appear in individuals. Requested inclusion of this property into RO. Check details here again after inclusion. This property might be better suited as a data property? If as a data property, perhaps there should be a standardised way of inputting age of onset? metadata complete - requires restrictions and relationships SCDO has age of onset A relation between a measure (e.g. a survey) and how the measure has been adapted cross-culturally. Requested inclusion of this property into RO. Check details here again after inclusion. Should be restricted to all measure/questionnaire classes. metadata complete - requires restrictions and relationships SCDO has cross-cultural adaptation A relationship between a condition/disease and a description of how the condition/disease is staged/graded. Requested inclusion of this property into RO. Check details here again after inclusion. metadata complete - requires restrictions and relationships SCDO Staging provided is disease/phenotype specific. has disease stage A relation between a measurement and a plan specification for obtaining the measurement that has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process. Requested inclusion of this property into RO. Check details here again after inclusion. To be applied to "Measurement", "Test, Method or Assay", "Therapeutics" metadata complete - requires restrictions and relationships SCDO has protocol A relation between a measure or measurement and the recommended procedure used by the measure or used to obtain the measurement. Requested inclusion of this property into RO. Check details here again after inclusion. metadata complete - requires restrictions and relationships SCDO has recommended procedure A relation between a measure (e.g. a survey) and the measure's respondents (people who respond). Respondents can be types or groups of people or people with a specific relationship to the main person of interest in the measure. Requested inclusion of this property into RO. Check details here again after inclusion. Should be restricted to all measure/questionnaire classes. no metadata complete - requires restrictions and relationships SCDO If the main person of interest responds, "Self" is indicated. If a person other than the main person of interest can respond, "Proxy" is indicated. If the proxy responder has a specific relationship (Family Members; Health Care Provider or Care-giver) to the main person of interest, that relationship should be indicated in brackets after "Proxy", e.g. Proxy (Health Care Provider or Care-giver). If more than one type of proxy responder is relevant, these should be listed and separated by ";", e.g. Proxy (Family Members; Health Care Provider or Care-giver) has respondents A relation between a measure (e.g. a survey) and the population that the measure was designed to target. Requested inclusion of this property into RO. Check details here again after inclusion. Should be restricted to all measure/questionnaire classes. metadata complete - requires restrictions and relationships SCDO Possible values used in the SCDO: Healthy Population; Clinic Patients (Children and/or Adults with SCD); Family Members; and/or Health Care Provider has target population An account of known translations of a measure into other languages (other than English). Requested inclusion of this property into RO. Check details here again after inclusion. Should be restricted to all measure/questionnaire classes. metadata complete - requires restrictions and relationships SCDO has translations A relation between a planned process and an objective it can be used to achieve. Requested inclusion of this property into RO. Check details here again after inclusion. This property is originally an object property. metadata complete - requires restrictions and relationships has_application_toward Eventually to be replaced by "is caused by" object property metadata incomplete is caused by A relationship between a condition (a phenotype or disease) and a description of distinctive characteristics or essential features. Requested inclusion of this property into RO. Check details here again after inclusion. metadata complete - requires restrictions and relationships SCDO is characterised by Description inherent in name (not provided by source) Only label adapted organizational term Used for properties, not classes. For classes, use "has curation status" object property. property has curation status A relation between a selected entity and the predefined criteria that were met by the entity and that made it eligible for selection. Requested inclusion of this property into RO. Check details here again after inclusion. Should be restricted to all measure/questionnaire classes. metadata complete - requires restrictions and relationships SCDO selection criteria met A relation between a measure and the age ranges for which the measure has been validated. Requested inclusion of this property into RO. Check details here again after inclusion. Should be restricted to all measure/questionnaire classes. metadata complete - requires restrictions and relationships SCDO validated for age ranges A relation between a measure (e.g. a survey) and an indication of whether the measure is freely available. Requested inclusion of this property into RO. Check details here again after inclusion. Should be restricted to all measure/questionnaire classes. metadata complete - requires restrictions and relationships SCDO 'yes' indicates that the measure is freely available. 'no' indicates that the measure is not freely available. freely available Records the slider label used by REDCap for a data element that uses a slider to collect data. SCDO (Jade Hotchkiss) has slider label curation status - complete curation status - incomplete An indication of whether or not a clinical code requires an additional code to be specified with it. Annotation is either "yes", "no" or "if applicable, X", where X is the name of a diagnosis for which a code should be provided if it is applicable. SCDO (Jade Hotchkiss) requires additional code An indication of whether a term/class already exists in other ontologies. Only used for term (descriptions) that were not taken directly from an existing ontology. SCDO (Jade Hotchkiss) Annotation options: Negligable Not relevant to context of sickle cell Few but definitions not freely available Suggest update to description Suggest update to label None existence in other ontologies Records the answer options text for input in Redcap for a data element that provides answer options. SCDO (Jade Hotchkiss) has answer options text Records the field label of a data element. SCDO (Jade Hotchkiss) has field label Records the variable of the associated data element from a REDCap data capture instrument. SCDO (Jade Hotchkiss) has redcap variable Records the section of a CRF in which a data element occurs. SCDO (Jade Hotchkiss) in CRF section Records the calculation used to automatically calculate the value for a data element in REDCap. SCDO (Jade Hotchkiss) has calculation equation Records a data element's field note (a note provided below the answer field). SCDO (Jade Hotchkiss) has field note Records the order in which a data element appears in a specific section of a specific CRF/questionnaire/instrument. This is provided in the form of a number which is relative to the order numbers of other data elements of the section. SCDO (Jade Hotchkiss) order in CRF section Used to provide a list of sections present in a questionnaire/instrument. SCDO (Jade Hotchkiss) has sections Records the type of validation used for a data element in REDCap. SCDO (Jade Hotchkiss) has redcap validation Records the branching logic applied to a data element in REDCap. SCDO (Jade Hotchkiss) has branching logic Records the mainimum value that is accepted for a data element that has validation applied to it in REDCap. SCDO (Jade Hotchkiss) has redcap min number validation Records the maximum value that is accepted for a data element that has validation applied to it in REDCap. SCDO (Jade Hotchkiss) has redcap max number validation Records the field annotations of a data element in REDCap. SCDO (Jade Hotchkiss) has redcap field annotation Used to show if a data element is considered an "identifier" (meaning it contains identifying information). SCDO (Jade Hotchkiss) is identifier Used to show if a data element is a required field. "y" is assigned to it if the data element is a required field. SCDO (Jade Hotchkiss) required field Records the custom alignment of a data element in REDCap. SCDO (Jade Hotchkiss) custom alignment Records a data element's field type, as per REDCap. SCDO (Jade Hotchkiss) has field type Used to record the matrix group that a data element occurs in. SCDO (Jade Hotchkiss) in matrix group An indication of whether or not a data element with a dropdown field should be autocompleted. Annotation is either "yes" or "no". SCDO (Jade Hotchkiss) autocomplete An indication of whether or not a data element with a slider field should display the slider's number values. Annotation is either "yes" or "no". SCDO (Jade Hotchkiss) show slider Used to record the identifier that had been used previously but is no longer in use. SCDO (Jade Hotchkiss) previous identifier A shortened form of a word or phrase, in this case a class/term. It consists of a group of letters taken from the word or phrase. yes metadata complete - requires restrictions and relationships abbreviation discarded/obsoleted synonym plural form layperson term A legal document giving official permission to do something with a Resource. no ontology annotation property dc:LicenseDocument License Document A summary of the resource. no ontology annotation property dc:abstract Abstract Information about who can access the resource or an indication of its security status. no ontology annotation property dc:accessRights Access Rights The method by which items are added to a collection. no ontology annotation property dc:accrualMethod Accrual Method The frequency with which items are added to a collection. no ontology annotation property dc:accrualPeriodicity Accrual Periodicity The policy governing the addition of items to a collection. no ontology annotation property dc:accrualPolicy Accrual Policy A class of entity for whom the resource is intended or useful. no ontology annotation property dc:audience Audience Date (often a range) that the resource became or will become available. no ontology annotation property dc:available Date Available An established standard to which the described resource conforms. no ontology annotation property dc:conformsTo Conforms To The spatial or temporal topic of the resource, the spatial applicability of the resource, or the jurisdiction under which the resource is relevant. no ontology annotation property dc:coverage Coverage An entity primarily responsible for making the resource. (This property is used in the SCDO when a term was created by the SCDO Working Group or a curator.) The SCDO uses this especially to apply to term descriptions. no ready for release dc:creator Creator A related resource that references, cites, or otherwise points to the described resource. no ontology annotation property dc:isReferencedBy Is Referenced By Date of formal issuance (e.g., publication) of the resource. no ontology annotation property dc:issued Date Issued A language of the resource. no ontology annotation property Recommended best practice is to use a controlled vocabulary such as RFC 4646 [RFC4646]. dc:language Language A legal document giving official permission to do something with the resource. no ontology annotation property dc:license License A related resource from which the described class/term's annotations are derived. yes pending vetting by the SCDO developers dc:source synonym_type_property An alias in which the alias is broader than the primary class name. Example: cell division is a broad synonym of cytokinesis. no pending vetting by the SCDO developers hasBroadSynonym A database cross-reference. An annotation which directs one to information contained within a database. metadata complete - requires restrictions and relationships SBO:0000554 DbXref Xref database cross-reference database_cross_reference db xref hasDbXref database cross reference An alias in which the alias exhibits true synonymy. Example: ornithine cycle is an exact synonym of urea cycle. no pending vetting by the SCDO developers hasExactSynonym An alias in which the alias is narrower than the primary class name. Example: pyrimidine-dimer repair by photolyase is a narrow synonym of photoreactive repair. no pending vetting by the SCDO developers hasNarrowSynonym An alias in which the alias is related to the primary class name, but not necessarily broader or narrower. Example: cytochrome bc1 complex is a related synonym of ubiquinol-cytochrome-c reductase activity; virulence is a related synonym of pathogenesis. no pending vetting by the SCDO developers hasRelatedSynonym An annotation property used to further annotate synonym axioms. has_synonym_type Additional information describing the class/term. yes rdfs:comment A human-readable name for the class/term. yes rdfs:label Further information about the class/term. yes rdfs:seeAlso The annotation property that indicates that a given entity has been deprecated. deprecated A preferred label. yes pending vetting by the SCDO developers skos:prefLabel A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). no metadata complete - requires restrictions and relationships RO:0002200 has phenotype Inverse of "has phenotype" object property. If required later, specify as inverse of "has phenotype" in Protege. no metadata complete - requires restrictions and relationships phenotype of A relation that holds between a disease or an organism and a phenotype that is a symptom (subjective evidence of disease perceived by the patient). Description adapted from RO. Suggest this description be updated in RO. RO:0002452 has symptom A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population. RO:0003306 contributes to frequency of condition A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition. RO:0003307 ameliorates condition A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition. RO:0003309 exacerbates condition A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity. RO:0003310 condition ameliorated by A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity. RO:0003311 condition exacerbated by A relationship between a phenotype and a disease modifier, where the disease modifier modifies the age of onset of the phenotype. Age of onset is defined as "The age group in which disease manifestations appear." (HPO) SCDO (Jade Hotchkiss) age of onset modified by A relation between a process (e.g. a form of therapy) and a medical device, where the medical device is used in the process. SCDO (Jade Hotchkiss) uses medical device A relationship between a condition (a phenotype or disease) and an entity (a genotype or genetic variation) where the entity has a causal role for the condition. SCDO (Jade Hotchkiss) caused or contributed to by A relationship between a phenotype and a disease modifier, where the disease modifier modifies the mortality (due to the phenotype) of the SCD sufferer. SCDO (Jade Hotchkiss) mortality modified by A relationship between a phenotype and a disease modifier, where the disease modifier modifies the temporal pattern of the phenotype. Temporal pattern is defined as "The speed at which disease manifestations appear and develop." (HPO) SCDO (Jade Hotchkiss) temporal pattern modified by A relation between a Diagnostic Tool (test, method, assay, etc.) or the Diagnostic Measurement obtained from such a tool and a specific Diagnostic Device, where the Diagnostic Device is used in the application of the Diagnostic Tool or to obtain the Diagnostic Measurement. SCDO (Jade Hotchkiss) has diagnostic device An object property that specifies the type of an ICD-10-CM code, whether Billable or Non-Billable. SCDO (Jade Hotchkiss) is ICD-10-CM code type A relationship that holds between a phenotype (i.e. manifestation) and a condition such as a disease (hemoglobinopathy), wherein the phenotype is evidence of the condition. SCDO (Jade Hotchkiss) manifestation of A relation between a phenotype that is a symptom (subjective evidence of disease perceived by the patient) and a disease. SCDO (Jade Hotchkiss) symptom of A relationship between 'a' and 'b', where 'a' has some causal role for 'b'. SCDO (Jade Hotchkiss) causes or contributes to A relation between a condition (Hemoglobinopathy) and a form of research (type of study) that the condition was studied in. SCDO (Jade Hotchkiss) studied in A relation between a condition (disease or phenotype) and a type of linking association (e.g. age of onset association). SCDO (Jade Hotchkiss) associated via A relation between a condition (disease or phenotype) and an aspect of an individual's life (personal attribute), behavior, an environmental exposure, or an inborn or inherited characteristic that increases the likelihood of the condition. SCDO (Jade Hotchkiss) has risk factor A relation between an aspect of an individual's life (personal attribute), behavior, an environmental exposure, or an inborn or inherited characteristic that increases the likelihood of a condition and the condition (disease or phenotype) that it increases the likelihood of. SCDO (Jade Hotchkiss) risk factor for A relationship between an Abnormal Phenotype that is a diagnosis of a condition and a Phenotype that is a finding from a Diagnostic Measurement, where the Phenotype that is a finding is used as evidence to diagnose patients with the Abnormal Phenotype that is a diagnosis. SCDO (Jade Hotchkiss) diagnosed using finding A relationship between a Diagnostic Measurement and the Unit of Measurement used for the values provided by the data properties that specify upper (ULN) or lower (LLN) limit of normal for the Diagnostic Measurement. None SCDO (Jade Hotchkiss) has reference range standard unit so:associated_with associated with Add properties that link diagnostic tools or measurements back to phenotypes..."diagnoses" when linked to a diagnosis? "detects" when linked to a phenotype that is a deviation from normal (e.g. an increased level of something). Used to record the lowest value of the range of statistical characteristics that are supposed to represent accepted standard, non-pathological pattern for particular laboratory result or other quantitative parameter. None has lower limit of normal has lower reference limit has LLN Used to record the top value of the range of statistical characteristics that are supposed to represent accepted standard, non-pathological pattern for particular laboratory result or other quantitative parameter. None has upper limit of normal has upper reference limit has ULN Records the minimum number of selections that a respondent is allowed to make from a list of multiple answer options provided for a data element. SCDO (Jade Hotchkiss) min number of selections allowed Records the maximum number of selections that a respondent is allowed to make from a list of multiple answer options provided for a data element. SCDO (Jade Hotchkiss) max number of selections allowed Used to record the lowest value of the range of statistical characteristics that are supposed to represent accepted standard, non-pathological pattern for males for a particular laboratory result or other quantitative parameter. None has lower limit of normal for males has LLN male Used to record the lowest value of the range of statistical characteristics that are supposed to represent accepted standard, non-pathological pattern for females for a particular laboratory result or other quantitative parameter. None has lower limit of normal for females has LLN female Used to record the lowest value of the range of statistical characteristics that are supposed to represent accepted standard, non-pathological pattern for children for a particular laboratory result or other quantitative parameter. None has lower limit of normal for children has LLN pediatric Used to record the top value of the range of statistical characteristics that are supposed to represent accepted standard, non-pathological pattern for males for a particular laboratory result or other quantitative parameter. None has upper limit of normal for males has ULN male Used to record the top value of the range of statistical characteristics that are supposed to represent accepted standard, non-pathological pattern for females for a particular laboratory result or other quantitative parameter. None has upper limit of normal for females has ULN female Used to record the top value of the range of statistical characteristics that are supposed to represent accepted standard, non-pathological pattern for children for a particular laboratory result or other quantitative parameter. None has upper limit of normal for children has ULN pediatric APOLLO_SV:00000241 An information content entity specifying the upper and lower limit of a range of ages of continuants. Sufficient SCDO:1000403 APOLLO_SV:00000241 Age Range Category ARO:0000006 Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure/function processes critical for life or replication are inhibited. http://purl.obolibrary.org/obo/ARO_0000006 Sufficient SCDO:0003119 ARO:0000006 Abomacetin Emgel Eritromicina Erymax Erythrocin Erythromycin A Erythromycine Erythromycinum N-methylerythromycin A Erythromycin ARO:0000054 Penicillin (sometimes abbreviated PCN) is a beta-lactam antibiotic used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms. It works by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Sufficient SCDO:0000880 ARO:0000054 PCN Penicillins Penicillin ARO:0000064 Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan. http://purl.obolibrary.org/obo/ARO_0000064 Sufficient SCDO:0002381 ARO:0000064 AMX Amolin Amopenixin Amoxicilina Amoxicilline Amoxicillinum Clamoxyl D-Amoxicillin Moxal Amoxycillin CHEBI:23888 Any substance which when absorbed into a living organism may modify one or more of its functions. The term is generally accepted for a substance taken for a therapeutic purpose, but is also commonly used for abused substances. Add sub-class "Iron Chelator" with sub-classes "Deferoxamine" and "Deferiprone" (see wikipedia page for "Beta Thalassemia"...mentions how they're used to treat beta thalassemia major). Also add "Deferoxamine" and "Deferiprone" below "Iron Chelation Therapy". Sufficient SCDO:1000200 CHEBI:23888 Drug CHEBI:35475 An anti-inflammatory drug that is not a steroid. In addition to anti-inflammatory actions, non-steroidal anti-inflammatory drugs have analgesic, antipyretic, and platelet-inhibitory actions. They act by blocking the synthesis of prostaglandins by inhibiting cyclooxygenase, which converts arachidonic acid to cyclic endoperoxides, precursors of prostaglandins. http://purl.obolibrary.org/obo/CHEBI_35475 Sufficient SCDO:0005809 CHEBI:35475 Non-Steroidal Anti-Inflammatory Agent Non-Steroidal Anti-Inflammatory Drug CHEBI:35482 A narcotic or opioid substance, synthetic or semisynthetic agent producing profound analgesia, drowsiness, and changes in mood. http://purl.obolibrary.org/obo/CHEBI_35482 Sufficient SCDO:0000836 CHEBI:35482 Opioid Analgesic Opioid CHEBI:35493 A drug that prevents or reduces fever by lowering the body temperature from a raised state. An antipyretic will not affect the normal body temperature if one does not have fever. Antipyretics cause the hypothalamus to override an interleukin-induced increase in temperature. The body will then work to lower the temperature and the result is a reduction in fever. http://purl.obolibrary.org/obo/CHEBI_35493 Sufficient SCDO:0005335 CHEBI:35493 Anti-Pyretic Antipyretic CHEBI:42797 A gamma-amino acid that is cyclohexane substituted at position 1 by aminomethyl and carboxymethyl groups. Used for treatment of neuropathic pain and restless legs syndrome. http://purl.obolibrary.org/obo/CHEBI_42797 Sufficient SCDO:0007493 CHEBI:42797 1-(Aminomethyl)cyclohexaneacetic acid Neurontin Gabapentin CHEBI:50858 A natural or synthetic analogue of the hormones secreted by the adrenal gland. Sufficient SCDO:0003901 CHEBI:50858 Corticoides Corticosteroides Corticosteroids Corticosteroid CHEBI:5790 An opioid analgesic derived from morphine and used mainly as an analgesic. It has a shorter duration of action and is more potent than morphine. http://www.drugbank.ca/drugs/DB00327 Sufficient SCDO:0000577 CHEBI:5790 3-hydroxy-17-methyl-4,5alpha-epoxymorphinan-6-one Hydromorphone CHEBI:60809 Any pharmacological or immunological agent that modifies the effect of other agents such as drugs or vaccines while having few if any direct effects when given by itself. http://purl.obolibrary.org/obo/CHEBI_60809 Sufficient SCDO:0000025 CHEBI:60809 Adjuvant Medicine Adjuvant CHEBI:6807 A synthetic opioid that is used as the hydrochloride. It is an opioid analgesic that is primarily a mu-opioid agonist. It has actions and uses similar to those of morphine. It also has a depressant action on the cough center and may be given to control intractable cough associated with terminal lung cancer. Methadone is also used as part of the treatment of dependence on opioid drugs, although prolonged use of methadone itself may result in dependence. http://www.drugbank.ca/drugs/DB00333 Sufficient SCDO:0000752 CHEBI:6807 6-(dimethylamino)-4,4-diphenylheptan-3-one Physeptone Methadone CHEBI:6909 A member of the class of imidazoles substituted at C-1, -2 and -5 with 2-hydroxyethyl, nitro and methyl groups respectively. It has activity against anaerobic bacteria and protozoa, and has a radiosensitising effect on hypoxic tumour cells. It may be given by mouth in tablets, or as the benzoate in an oral suspension. The hydrochloride salt can be used in intravenous infusions. Metronidazole is a prodrug and is selective for anaerobic bacteria due to their ability to intracellularly reduce the nitro group of metronidazole to give nitroso-containing intermediates. These can covalently bind to DNA, disrupting its helical structure, inducing DNA strand breaks and inhibiting bacterial nucleic acid synthesis, ultimately resulting in bacterial cell death. http://purl.obolibrary.org/obo/CHEBI_6909 Sufficient SCDO:0002912 CHEBI:6909 Satric Trichazol Metronidazole CHEBI:7852 A semisynthetic derivative of codeine that acts as a narcotic analgesic more potent and addicting than codeine. http://www.drugbank.ca/drugs/DB00497 Sufficient SCDO:0000847 CHEBI:7852 14-hydroxy-3-methoxy-17-methyl-4,5alpha-epoxymorphinan-6-one Dihydrone An extended-release (ER) form of oxycodone (Xtampza ER) was approved for the management of daily, around-the-clock pain management in April, 2016. Oxycodone CHMO:0001009 Column chromatography where the mobile phase is a liquid, the stationary phase consists of very small particles and the inlet pressure is relatively high. Perhaps change label to "Hemoglobin by High Performance Liquid Chromatography"? See dc:source provided. http://purl.obolibrary.org/obo/CHMO_0001009 Sufficient SCDO:0000563 CHMO:0001009 HPLC High Performance Liquid Chromatography High Pressure Liquid Chromatography High-Pressure Liquid Chromatography High-Performance Liquid Chromatography CHMO:0002580 A test which produces colour change in the sample. http://purl.obolibrary.org/obo/CHMO_0002580 Sufficient SCDO:0000264 CHMO:0002580 Colorimetric Test CMO:0000001 Any value resulting from the quantification of a morphological or physiological parameter pertaining to the heart and/or blood vessels. http://purl.obolibrary.org/obo/CMO_0000001 Sufficient SCDO:0000186 CMO:0000001 Cardiovascular Measurement CMO:0000003 Measurement of the pressure, or force per area, exerted by circulating blood against the walls of the blood vessels. The pressure is dependent on the energy of the heart action, elasticity of the vessel walls and volume and viscosity of the blood. There are many more specific sub-classes in the CMO. Are there any we want to include here? http://purl.obolibrary.org/obo/CMO_0000003 Sufficient SCDO:0000144 CMO:0000003 Blood Pressure Measurement CMO:0000011 Morphological measurement involving the entire body of an organism. http://purl.obolibrary.org/obo/CMO_0000011 Sufficient SCDO:0001245 CMO:0000011 Whole Body Morphological Measurement CMO:0000015 The level of heat in an organism. Sufficient SCDO:0000151 CMO:0000015 Body Temperature CMO:0000021 Measurement of the structure or forms of the entire body or parts of the body of an organism. Include the term "Body Composition" from PhenX? -- -- Any other relevant terms missing as sub-classes here? http://purl.obolibrary.org/obo/CMO_0000021 Sufficient SCDO:0000150 CMO:0000021 Anthropometric Measurement Anthropometrics Morphometry Body Morphological Measurement CMO:0000023 A quantification of a parameter of the chemical composition of blood. http://purl.obolibrary.org/obo/CMO_0000023 Sufficient SCDO:0000136 CMO:0000023 Blood Chemistry Measurement CMO:0000025 The number of red blood cells in a specified volume of blood most commonly 1 cubic millimeter (i.e. 1 microliter) of peripheral venous blood. http://purl.obolibrary.org/obo/CMO_0000025 Sufficient SCDO:0000973 CMO:0000025 Erythrocyte Count Erythrocyte Number Erythrocyte Numbers Red Blood Count Red Blood Cell Count CMO:0000027 The number of white blood cells in a specified volume of blood. http://purl.obolibrary.org/obo/CMO_0000027 Sufficient SCDO:0001243 CMO:0000027 Leukocyte Count White Corpuscle Count White Blood Cell Count CMO:0000029 The number of platelets (thrombocytes) in a specified volume of blood, usually expressed as platelets per cubic millimeter of whole blood. http://purl.obolibrary.org/obo/CMO_0000029 Sufficient SCDO:0000906 CMO:0000029 Blood Platelet Number Blood Platelet count Platelet Number Platelet Count CMO:0000030 The number of granulocytes categorized as neutrophils in a specified volume of blood. A neutrophil is, or is in the process of becoming, a granular leucocyte having a nucleus with three to five lobes connected by threads of chromatin, cytoplasm containing very fine granules, and which is readily stainable with neutral dyes. Sufficient SCDO:1000442 CMO:0000030 Neutrophil Granulocyte Count Blood Neutrophil Count CMO:0000035 A measurement of the blood, it's contents, cells or other factors contained within the blood. http://purl.obolibrary.org/obo/CMO_0000035 Sufficient SCDO:0000143 CMO:0000035 Blood Measurement CMO:0000036 A value resulting from the quantification of a morphological or physiological parameter of blood cells, i.e. cells native to the circulation, including those of erythroid, lymphoid, myeloid and monocytic lineages. A cell is a membrane-enclosed protoplasmic mass constituting the smallest structural unit of an organism that is capable of independent functioning. Perhaps include missing sub-classes of "Blood Cell Measurement" from the Clinical Measurement Ontology? http://purl.obolibrary.org/obo/CMO_0000036 Sufficient SCDO:0000135 CMO:0000036 Blood Cell Measurement CMO:0000037 Percentage of total blood volume that is made up of red blood cells. http://purl.obolibrary.org/obo/CMO_0000037 Sufficient SCDO:0000503 CMO:0000037 Hct Packed Cell Volume Packed Red Blood Cell Volume Hematocrit CMO:0000038 A measure of the average volume or size of a single red blood cell. It is derived by dividing the total volume of packed red blood cells by the total red blood cell count. http://purl.obolibrary.org/obo/CMO_0000038 Sufficient SCDO:0000723 CMO:0000038 MCV Mean Cell Volume Mean Corpuscular Volume CMO:0000057 The amount of creatinine, a catabolic product of creatine phosphate used in skeletal muscle contraction found in a specified volume of serum. Link to "Glomerular Filtration Rate"... which object property? Create a new one and suggest to RO? "used to calculate"? Sufficient SCDO:0001042 CMO:0000057 Creatinine Level Serum Creatinine Level CMO:0000094 A measurement to assess the morphological or physiological state of the respiratory system or portion of the respiratory system. http://purl.obolibrary.org/obo/CMO_0000094 Sufficient SCDO:0000995 CMO:0000094 Respiratory System Measurement CMO:0000111 The number of granulocytes (polymorphonuclear leukocytes) in a specified volume of blood, usually 1 cubic millimeter. Sufficient SCDO:1000441 CMO:0000111 Blood Granulocyte Count CMO:0000123 The amount of bilirubin found in a specific volume of blood. http://purl.obolibrary.org/obo/CMO_0000123 Sufficient SCDO:0000134 CMO:0000123 Bilirubin Level Blood Bilirubin Level CMO:0000195 Any measurement of the movement of blood through the heart and blood vessels. Add any more from below "circulation measurement" in the CMO? Suggest to CMO "Blood Flow Measurement" be an exact synonym of "Circulation Measurement", as we have made it here. Suggest to CRISP that their "blood flow measurement" instead be "Blood Flow Test". Sufficient SCDO:0000142 CMO:0000195 Circulation Measurement Blood Flow Measurement CMO:0000204 Measurement to assess the sequential process through which multiple factors of the blood interact to form an insoluble fibrin clot. Add other sub-classes of "Blood Coagulation Measurement" from the CMO? blood fibrinogen level? thrombin time? activated clotting time (ACT)? platelet aggregation measurement? bleeding time (BT)? http://purl.obolibrary.org/obo/CMO_0000204 Sufficient SCDO:0000137 CMO:0000204 Blood Coagulation Measurement CMO:0000210 The time needed for plasma to form a fibrin clot after the addition of calcium and a phospholipid reagent. It is used to evaluate the intrinsic clotting system. Sufficient SCDO:0000014 CMO:0000210 APTT; Quick Activated Partial Thromboplastin Time CMO:0000211 Measurement of the clotting ability of fibrinogen, prothrombin, proaccelerin, proconvertin and Stuart factor, usually given in seconds to formation of clot after the addition of a tissue factor or thromboplastin. Sufficient SCDO:0000933 CMO:0000211 PTT Prothrombin Time CMO:0000225 Any measurement of a gas or gases dissolved in arterial blood, that is, blood which has absorbed oxygen in the lungs, including oxygen, nitrogen carbon dioxide and/or hydrogen. Sufficient SCDO:1000718 CMO:0000225 Arterial Blood Gas Measurement CMO:0000256 Any measurement of urine, the fluid waste product excreted by the kidneys, or its components. http://purl.obolibrary.org/obo/CMO_0000256 Sufficient SCDO:0001214 CMO:0000256 Urine Measurement CMO:0000283 The force per unit area attributable to the carbon dioxide, a colorless, odorless, incombustible gas formed during respiration and composed of one atom of carbon and two atoms of oxygen, dissolved in a specified volume of blood, defined as the force per unit area exerted by carbon dioxide in a mixture of gases in equilibrium with such a sample of blood at the same temperature. Sufficient SCDO:1000719 CMO:0000283 PaCO2 Partial Pressure of Blood Carbon Dioxide Partial Pressure of Blood Carbon Dioxide (Pco2) Partial Pressure of Carbon Dioxide (PaCO2) Pco2 Partial Pressure of Carbon Dioxide CMO:0000290 The average amount of hemoglobin per red blood cell calculated by dividing the total mass of hemoglobin by the number of red blood cells in a volume of blood. http://purl.obolibrary.org/obo/CMO_0000290 Sufficient SCDO:0000722 CMO:0000290 MCH Mean Cell Hemoglobin Mean Cell Hemoglobin Level Mean Corpuscular Haemoglobin Mean Corpuscular Haemoglobin Level Mean Corpuscular Hemoglobin Mean Corpuscular Hemoglobin Level CMO:0000291 The amount of hemoglobin in a given volume of packed red blood cells and is often calculated by dividing the hemoglobin concentration by the hematocrit. Add the sub-class "mean corpuscular sickle hemoglobin concentration (MCSHC)"? (see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC290884/pdf/jcinvest00309-0076.pdf) http://purl.obolibrary.org/obo/CMO_0000291 Sufficient SCDO:0000721 CMO:0000291 MCHC Mean Cell Hemoglobin Concentration Mean Corpuscular Haemoglobin Concentration Mean Corpuscular Hemoglobin Concentration CMO:0000364 The calculation of the cellular elements of the blood, usually including cell counts for white and red blood cells and platelets. http://purl.obolibrary.org/obo/CMO_0000364 PhenX protocol: Complete Blood Count #220501 Sufficient SCDO:0000270 CMO:0000364 Blood Cell Count Blood Cell Number CBC FBC Full Blood Count Complete Blood Count CMO:0000365 The total number of leukocytes in 1 cubic millimeter of peripheral venous blood. http://purl.obolibrary.org/obo/CMO_0000365 Sufficient SCDO:0001163 CMO:0000365 Total White Blood Cell Count CMO:0000366 The number of each type of leukocyte present in a specific volume of blood, usually 1 cubic millimeter. Perhaps add sub-classes from "Clinical Measurement Ontology"? http://purl.obolibrary.org/obo/CMO_0000366 Sufficient SCDO:0000140 CMO:0000366 Blood Differential Leukocyte Count Blood Differential WBC Count WBC Differential Count Blood Differential White Blood Cell Count CMO:0000376 The complete or entire amount of bilirubin in a specified volume of serum, the clear liquid that separates from blood after it has clotted completely, i.e. blood plasma from which fibrinogen has been removed. Bilirubin is the bile pigment produced by breakdown of heme and reduction of biliverdin. Sufficient SCDO:1000500 CMO:0000376 Total Serum Bilirubin Level CMO:0000506 The amount of hemoglobin, the red oxygen-carrying pigment of erythrocytes, in a specified volume of blood, as calculated from the optical density of a solution of lysed red cells in which hemoglobin has been converted to cyanomethemoglobin and measured with a spectrophotometer. Sufficient SCDO:0000523 CMO:0000506 Hbtotal Hemoglobin Level Total Hemoglobin Total Hemoglobin (Hbtotal) ctHB Hemoglobin Concentration CMO:0000507 The optical density as calculated from the intensity of light at a specified wavelength as it passes through a solution of lysed red blood cells. Sufficient SCDO:1000249 CMO:0000507 Hemoglobin Absorbance CMO:0000508 A measure of the oxygen carrying pigment of erythrocytes. http://purl.obolibrary.org/obo/CMO_0000508 Sufficient SCDO:0000543 CMO:0000508 Hemoglobin Measurement CMO:0000665 Pressure exerted by the heart muscle in its maximally contracted state. http://purl.obolibrary.org/obo/CMO_0000665 Sufficient SCDO:0000499 CMO:0000665 Heart Contraction Pressure CMO:0000921 Any measurement of platelets, the disk-shaped structures found in the blood of mammals which play a vital role in blood coagulation. Platelets lack nuclei and DNA but contain active enzymes and mitochondria. http://purl.obolibrary.org/obo/CMO_0000921 Sufficient SCDO:0000907 CMO:0000921 Platelet Measurement CMO:0001321 Any measurement of a gas or gases dissolved in the blood, including oxygen, nitrogen carbon dioxide and/or hydrogen. Sufficient SCDO:1000312 CMO:0001321 Blood Gas Measurement CMO:0001324 The amount of oxygen bound to hemoglobin in the blood expressed as a percentage of the maximal binding capacity. Sufficient SCDO:0000848 CMO:0001324 HbO2 Oxyhemoglobin Saturation Oxyhemoglobin Saturation (HbO2) SO2 SaO2 Sats Oxygen Saturation CMO:0001356 Any measurement of a single red blood cell, one of the hemoglobin-containing blood cells that transport oxygen and carbon dioxide to and from the tissues, or of all of the red blood cells in a sample of blood. http://purl.obolibrary.org/obo/CMO_0001356 Sufficient SCDO:0000974 CMO:0001356 Erythrocyte Measurement Red Blood Cell Measurement CMO:0002079 The heaviness or degree to which the entire body of an organism at the point of or shortly after birth is drawn to the earth by gravity. Sufficient SCDO:1000311 CMO:0002079 Body Weight of Neonate Neonatal Body Weight Birth Weight CMO:0002341 Any value resulting from the quantification of a morphological or physiological parameter of leukocytes, largely colorless blood corpuscles capable of ameboid movement, whose chief function is to protect the body against microorganisms and other disease-causing entities. http://purl.obolibrary.org/obo/CMO_0002341 Sufficient SCDO:0001244 CMO:0002341 White Blood Cell Measurement CMO:0002520 Measurement of the amount of haptoglobin in a specified sample of serum, the clear liquid that separates from blood after it has clotted completely, i.e. blood plasma from which fibrinogen has been removed. Haptoglobin is a serum alpha2 globulin glycoprotein, produced by the liver, that functions to bind free plasma hemoglobin, which allows degradative enzymes to gain access to the hemoglobin, while at the same time preventing loss of iron through the kidneys and protecting the kidneys from damage by hemoglobin. Sufficient SCDO:0000467 CMO:0002520 Haptoglobin Level Haptoglobin Levels Serum Haptoglobin Level CMO:0002876 The amount of N-terminal (NT)-pro hormone BNP (Nppb) in a specified volume of blood. Value given as 1 Decimal Place Nanogram per Liter (according to PhenX https://www.phenxtoolkit.org/protocols/view/810501) associated with acute congestive heart failure (http://www.ebi.ac.uk/efo/EFO_0004745) Sufficient SCDO:0000786 CMO:0002876 BNPT Level Blood NH2-Terminal pro-B-Type Natriuretic Peptide Level N-Terminal Prohormone of Brain Natriuretic Peptide Level NT-proBNP Level NT-proBNP Measurement N-Terminal Pro-Brain Natriuretic Peptide Level DOID:0050731 A vitamin metabolic disorder that results from low blood levels of vitamin B12. Sufficient SCDO:0005733 DOID:0050731 Cobalamin Deficiency Hypocobalaminemia Vitamin B12 Deficiency DOID:0060181 A colitis caused by inadequate blood supply to the colon. Is diagnosed by: abdominal computed tomography scan http://purl.obolibrary.org/obo/DOID_0060181 Sufficient SCDO:0002870 DOID:0060181 Ischemic Cholitis DOID:0111033 A hemochromatosis characterized by a predisposition to iron loading that is exacerbated by excessive intake of dietary iron, commonly related to consumption of tradition beer brewed in non-galvanized steel drums. Sufficient SCDO:1000282 DOID:0111033 Bantu Siderosis Iron Overload in Africa African Iron Overload DOID:1188 A neuropathy that is characterized by damage to a single nerve, which results in loss of movement, sensation, or other function of that nerve. Sufficient SCDO:0000769 DOID:1188 Single Damaged Nerve Mononeuropathy DOID:1584 A lung disease that involves a vasoocclusive crisis of the pulmonary vasculature seen in patients with sickle cell anemia. The crisis is initiated by a lung infection, and the resulting inflammation and loss of oxygen tension leads to sickling of red cells and further vasoocclusion. This definition was given by the WG: 'Acute onset of respiratory symptoms and/or signs and an X-ray consistent with alveolar consolidation but not atelectasis, involving at least one complete lung segment." With this definition source:The acute chest syndrome in sickle cell disease: incidence and risk factors. The Cooperative Study of Sickle Cell Disease. O. Castro, D. J. Brambilla, B. Thorington, C. A. Reindorf, R. B. Scott, P. Gillette, J. C. Vera, P. S. Levy Blood. 1994 Jul 15; 84(2): 643–649. However, the definition did not seem to come from this source, so the DO term was used instead. Sufficient SCDO:0000015 DOID:1584 Acute Chest Syndrome in Sickle Cell Disease From the DO: The disease has_symptom fever, has_symptom pleuritic chest pain, has_symptom tachypnea, has_symptom cough, has_symptom hypoxemia, has_symptom marked leukocytosis, has_symptom marked leukocytosis, and has_symptom diffuse infiltrates on chest radiograph. Acute Chest Syndrome DOID:1826 A brain disease that is characterized by the occurrance of at least two unprovoked seizures resulting from a persistent epileptogenic abnormality of the brain that is able to spontaneously generate paroxysmal activity and typically manifested by sudden brief episodes of altered or diminished consciousness, involuntary movements, or convulsions. http://purl.obolibrary.org/obo/DOID_1826 Sufficient SCDO:0008484 DOID:1826 Epilepsy DOID:2326 A gastrointestinal system infectious disease that involves inflammation of the lining of the stomach and small and large intestines, which is caused by viruses, bacteria, or parasites. Chemicals and drugs also cause gastroenteritis. The symptoms include diarrhea, loss of appetite, nausea, vomiting, cramps, and discomfort in the abdomen. http://purl.obolibrary.org/obo/DOID_2326 Sufficient SCDO:0007198 DOID:2326 Gastroenteritis DOID:4 A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. http://purl.obolibrary.org/obo/DOID_4 Sufficient SCDO:0001365 DOID:4 Disease DOID:813 An arthritis that involves infection by a pathogen located in a joint. http://purl.obolibrary.org/obo/DOID_813 Sufficient SCDO:0002067 DOID:813 Infected Joint Infectious Arthritis Septic Arthritis DOID:9220 A sleep apnea that is characterized by a malfunction of the basic neurological controls for breathing rate and the failure to give the signal to inhale, causing the individual to miss one or more cycles of breathing. http://purl.obolibrary.org/obo/DOID_9220 Sufficient SCDO:0000200 DOID:9220 Primary Central Sleep Apnea Central Sleep Apnea DRON:00017565 A nasal vasoconstricting decongestant drug which acts by binding to the same receptors as adrenaline. It is applied as a spray or as drops into the nose to ease inflammation and congestion of the nasal passageways. It binds alpha-adrenergic receptors to activate the adrenal system which causes systemic vasoconstriction, thereby easing nasal congestion. http://www.drugbank.ca/drugs/DB06694 Sufficient SCDO:0001254 DRON:00017565 Balminil Otrivin Xylomethazoline Xylometazoline DUO:0000018 This requirement indicates that use of the data is limited to not-for-profit organizations and not-for-profit use, non-commercial use. Sufficient SCDO:1000413 DUO:0000018 Not for Profit Use Only DUO:0000019 This requirement indicates that requestor agrees to make results of studies using the data available to the larger scientific community. Sufficient SCDO:1000416 DUO:0000019 Publication Required DUO:0000020 This could be coupled with a string describing the primary study investigator(s). Sufficient SCDO:1000409 DUO:0000020 Collaboration Required DUO:0000021 This requirement indicates that the requestor must provide documentation of local IRB/ERB approval. Sufficient SCDO:1000410 DUO:0000021 Ethics Approval Required DUO:0000022 This should be coupled with an ontology term describing the geographical location the restriction applies to. Sufficient SCDO:1000411 DUO:0000022 Geographical Restriction DUO:0000024 This should be coupled with a date specified as ISO8601 Sufficient SCDO:1000415 DUO:0000024 Publication Moratorium DUO:0000025 This should be coupled with an integer value indicating the number of months. Sufficient SCDO:1000418 DUO:0000025 Time Limit on Use DUO:0000026 This requirement indicates that use is limited to use by approved users. Sufficient SCDO:1000419 DUO:0000026 User Specific Restriction DUO:0000027 This requirement indicates that use is limited to use within an approved project. Sufficient SCDO:1000414 DUO:0000027 Project Specific Restriction DUO:0000028 This requirement indicates that use is limited to use within an approved institution. Sufficient SCDO:1000412 DUO:0000028 Institution Specific Restriction DUO:0000029 This requirement indicates that the requestor must return derived/enriched data to the database/resource. Sufficient SCDO:1000417 DUO:0000029 Return to Database or Resource ENVO:02500036 An environmental system process that results in the introduction of contaminants into an environment. http://purl.obolibrary.org/obo/ENVO_02500036 Sufficient SCDO:0000912 ENVO:02500036 Environmental Pollution Pollution EUPATH:0000034 A genotype information which is about the presence and degree of alpha-thalassemia, a form of thalassemia involving the number of functional HBA1 and HBA2 genes. Sufficient SCDO:1000216 EUPATH:0000034 Alpha Thalassemia Genotype EUPATH:0000050 A clinical visit that is primarily for a regular examination. Sufficient SCDO:1000848 EUPATH:0000050 Routine Clinical Visit EUPATH:0000215 An anemia with hemoglobin levels less than 5 gm/dL. http://purl.obolibrary.org/obo/EUPATH_0000215 Sufficient SCDO:1000055 EUPATH:0000215 Severe Anemia EUPATH:0000310 An information content entity that is about a clinical visit. Sufficient SCDO:1000851 EUPATH:0000310 Information on Observation Details EUPATH:0021227 A scalar measurement datum of the concentration of urea in blood that is a specified output of a blood test. Sufficient SCDO:1000603 EUPATH:0021227 Serum Urea Concentration Blood Urea Concentration ExO:0000034 An individual attribute that is the usual or principal work or business of an individual. http://purl.obolibrary.org/obo/ExO_0000034 Sufficient SCDO:0000821 ExO:0000034 Career Employment Job Vocation Occupation ExO:0000048 Human-made surroundings that provide the setting for human activity, ranging in scale from personal shelter and buildings to neighborhoods and cite, and can often include their supporting infrastructure, such as water supply or energy networks. Sufficient SCDO:0000167 ExO:0000048 Built Environment GAZ:00000448 A reference to a place on the Earth, by its name or by its geographical location. http://purl.obolibrary.org/obo/GAZ_00000448 Sufficient SCDO:0000451 GAZ:00000448 Geographic Region Geographic Location GSSO:000109 Intersex is an umbrella term with a complex history. It is usually used to refer to persons with congenital conditions which involve differences in the many intertwined processes of sexual development. Sufficient SCDO:1000672 GSSO:000109 Intersex GSSO:003239 Principles which provide a framework within which ethical dilemmas and other problems may be analyzed. Sufficient SCDO:1000427 GSSO:003239 Ethical Principle HP:0000005 The pattern in which a particular genetic trait or disorder is passed from one generation to the next. http://purl.obolibrary.org/obo/HP_0000005 Sufficient SCDO:0001367 HP:0000005 Inheritance Mode of Inheritance HP:0000006 A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in heterozygotes. In the context of medical genetics, an autosomal dominant disorder is caused when a single copy of the mutant allele is present. Males and females are affected equally, and can both transmit the disorder with a risk of 50% for each child of inheriting the mutant allele. Sufficient SCDO:1000140 HP:0000006 Autosomal Dominant Form Autosomal Dominant Inheritance Autosomal Dominant Predisposition Autosomal Dominant HP:0000007 A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in individuals with two pathogenic alleles, either homozygous (two copies of the same mutant allele) or compound heterozygous (whereby each copy of a gene has a distinct mutant allele). http://purl.obolibrary.org/obo/HP_0000007 Sufficient SCDO:0001368 HP:0000007 Autosomal Recessive Form Autosomal Recessive Inheritance Autosomal Recessive Predisposition Autosomal Recessive HP:0000027 Absence of any measurable level of sperm in a male's semen. Sufficient SCDO:0000092 HP:0000027 Absent Sperm in Semen Azoospermia HP:0000044 Hypogonadotropic hypogonadism is characterized by reduced function of the gonads (testes in males or ovaries in females) and results from the absence of the gonadal stimulating pituitary hormones: follicle stimulating hormone (FSH) and luteinizing hormone (LH). Sufficient SCDO:0002903 HP:0000044 Hypogonadotropic Hypogonadism Secondary Hypogonadism Hypogonadotropic Hypogonadism HP:0000077 An abnormality of the kidney. http://purl.obolibrary.org/obo/HP_0000077 Sufficient SCDO:0002133 HP:0000077 Abnormal Kidney Anomaly of the Kidney Renal Anomaly Abnormality of the Kidney HP:0000078 An abnormality of the genital system. Sufficient SCDO:1000263 HP:0000078 Genital Abnormalities Genital Abnormality Genital Anomalies Genital Defects Abnormality of the Genital System HP:0000079 An abnormality of the urinary system. Sufficient SCDO:0001347 HP:0000079 Anomaly of the Urinary System Urinary Tract Abnormalities Urinary Tract Abnormality Urinary Tract Anomalies Urinary Tract Anomaly Abnormality of the Urinary System HP:0000080 An abnormal functionality of the genital system. Sufficient SCDO:1000270 HP:0000080 Abnormality of Genital Physiology Abnormality of Reproductive System Physiology HP:0000084 Failure of the kidneys to adequately filter toxins and waste products from the blood; classified as acute (as in acute kidney injury) or chronic (as in chronic kidney disease); a number of other diseases or health problems may cause either form of renal failure to occur. http://purl.obolibrary.org/obo/MP_0003606 Variable May be Acute (acute kidney injury) or chronic (chronic kidney disease). Has a variety of causes - dependent upon acuity - see definitions for acute kidney injury (acute renal failure) and chronic kidney disease. Sufficient SCDO:0000674 HP:0000084 Renal Failure Renal Insufficiency Treatment is dependent upon etiology and acuity. If refractory to medical therapy, renal replacement or dialysis may be indicated. Kidney Failure HP:0000096 Scarring and fibrosis within the glomerulus. Any form of injury to the kidney can lead to glomerulosclerosis. Histologically noted by scarring and fibrosis in the glomerulus. Sufficient SCDO:0000460 NHLBI 2014 Guidelines HP:0000096 Glomerular Sclerosis Renal Glomerular Fibrosis Glomerulosclerosis HP:0000097 Segmental accumulation of scar tissue in individual (but not all) glomeruli. Sufficient SCDO:0009968 HP:0000097 Focal Glomerulosclerosis Focal and Segmental Glomerular Sclerosis Focal and Segmental Glomerulosclerosis Focal Segmental Glomerulosclerosis HP:0000099 Inflammation of the renal glomeruli. Provide source for additional info. May occur at any age. Variety of causes - in sickle cell disease, most common lesion is focal segmental glomerulosclerosis (FSGS) but also reported Membranoproliferative glomerulonephritis and other forms of glomerulonephritis. Patients with hematuria may have dark-colored urine. Glomerulonephritis may lead to the proteinuria and "foamy" appearance of the urine. If the latter is substantial, patients may develop clinically evident edema. Sufficient SCDO:0000458 HP:0000099 GN Glomerular Nephritis Glomerulonephritis HP:0000112 A nonspecific term referring to disease or damage of the kidneys. Sufficient SCDO:0000795 HP:0000112 Kidney Damage Kidney Disease Nephropathy HP:0000118 A phenotype that shows detectable differences from normal. http://purl.obolibrary.org/obo/FYPO_0001985 Sufficient SCDO:0009818 HP:0000118 Phenotypic Abnormality Abnormal Phenotype HP:0000123 The presence of inflammation affecting the kidney. Provide source for additional info. May be caused by autoimmune disease, allergic responses, toxic injury, infectious causes. May be associated with loss of kidney function, pyuria or hematuria, and proteinuria dependent upon cause. Sufficient SCDO:0000793 HP:0000123 Kidney Inflammation Nephritis HP:0000132 Prolonged and/or excessive menses at regular intervals in excess of 80 ml or lasting longer than 7 days. Provide source for additional info. http://purl.obolibrary.org/obo/HP_0000132 Sufficient SCDO:0000745 HP:0000132 Abnormally Heavy Bleeding During Menstruation Hypermenorrhea Menorrhagia HP:0000225 Hemorrhage affecting the gingiva. http://purl.obolibrary.org/obo/HP_0000225 Sufficient SCDO:0000452 HP:0000225 Bleeding Gums Gingival Hemorrhage Gingivorrhagia Gingival Bleeding HP:0000271 An abnormality of the face. http://purl.obolibrary.org/obo/HP_0000271 Sufficient SCDO:0003024 HP:0000271 Facial Abnormality Abnormality of the Face HP:0000388 Inflammation or infection of the middle ear. Source needed for additional information. http://purl.obolibrary.org/obo/HP_0000388 Sufficient SCDO:0000846 HP:0000388 is caused by: Usually bacterial but can be caused by fungus or virus infection. is characterised by: Pain or discharge from one or both ears Otitis Media HP:0000478 Any abnormality of the eye, including location, spacing, and intraocular abnormalities. Sufficient SCDO:1000294 HP:0000478 Abnormality of the Eye HP:0000505 Visual impairment (or vision impairment) is vision loss (of a person) to such a degree as to qualify as an additional support need through a significant limitation of visual capability resulting from either disease, trauma, or congenital or degenerative conditions that cannot be corrected by conventional means, such as refractive correction, medication, or surgery. Sufficient SCDO:1000022 HP:0000505 Impaired Vision Impaired Visual Function Loss of Eyesight Poor Vision Visual Impairment HP:0000618 Blindness is the condition of lacking visual perception defined as visual perception below 3/60 and/or a visual field of no greater than 10 degress in radius around central fixation. Sufficient SCDO:1000021 HP:0000618 Total Vision Loss Blindness HP:0000707 Any abnormality of the nervous system. http://purl.obolibrary.org/obo/HP_0000707 Sufficient SCDO:0009698 HP:0000707 Brain and/or Spinal Cord Issue Neurologic Abnormalities Neurological Abnormality Abnormality of the Nervous System HP:0000708 An abnormality of mental functioning including various affective, behavioural, cognitive and perceptual abnormalities. Include "Poor School Performance" as a sub-class. http://purl.obolibrary.org/obo/HP_0000708 Sufficient SCDO:0000105 HP:0000708 Behavioral Abnormality Behavioural Abnormality Behavioural Changes Behavioural Disorders Behavioural Disturbances Behavioural Problems Behavioural Symptoms Behavioural/Psychiatric Abnormalities Behavioural/Psychiatric Abnormality Psychiatric Disorders Psychiatric Disturbances Behavioural Abnormality HP:0000726 A loss of global cognitive ability of sufficient amount to interfere with normal social or occupational function. Dementia represents a loss of previously present cognitive abilities, generally in adults, and can affect memory, thinking, language, judgment, and behavior. Check and show which source was used for the description and whether the description was adapted from the source. -- Provide source for additional info. Sufficient SCDO:0000345 HP:0000726 Dementia, Progressive Progressive Dementia Dementia HP:0000763 Peripheral neuropathy affecting the sensory nerves. http://purl.obolibrary.org/obo/HP_0000763 Sufficient SCDO:0001038 HP:0000763 Peripheral Sensory Neuropathy Sensory Neuropathy HP:0000789 Inability to produce live offspring. Sufficient SCDO:0000639 HP:0000789 Sterility Infertility HP:0000798 Reduced count of spermatozoa in the semen, defined as a sperm count below 20 million per milliliter semen. Sufficient SCDO:0000827 HP:0000798 Low Sperm Count Oligospermia HP:0000805 Lack of the ability to control the urinary bladder leading to involuntary urination at an age where control of the bladder should already be possible. http://purl.obolibrary.org/obo/HP_0000805 Sufficient SCDO:0000434 HP:0000805 Enuresis HP:0000815 Reduced function of the gonads (testes in males or ovaries in females) associated with excess pituitary gonadotropin secretion and resulting in delayed sexual development and growth delay. Provide source for additional info. http://purl.obolibrary.org/obo/HP_0000815 Sufficient SCDO:0000586 HP:0000815 Hypergonadotrophic Hypogonadism Primary Hypogonadism Hypergonadotropic Hypogonadism HP:0000818 An abnormality of the endocrine system. Sufficient SCDO:0002780 HP:0000818 Abnormality of the Endocrine System HP:0000819 A group of abnormalities characterized by hyperglycemia and glucose intolerance. http://purl.obolibrary.org/obo/HP_0000819 Sufficient SCDO:0000367 HP:0000819 Diabetes Mellitus HP:0000820 An abnormality of the thyroid gland. Sufficient SCDO:1000278 HP:0000820 Thyroid Abnormality Abnormality of the Thyroid Gland HP:0000821 Deficiency of thyroid hormone. Provide source for additional info. http://purl.obolibrary.org/obo/HP_0000821 Sufficient SCDO:0000603 HP:0000821 Low T4 Underactive Thyroid Hypothyroidism HP:0000822 The presence of chronic increased pressure in the systemic arterial system. Sufficient SCDO:0008801 HP:0000822 Hypertension HP:0000823 Passing the age when puberty normally occurs with no physical or hormonal signs of the onset of puberty. Sufficient SCDO:0000342 HP:0000823 Delayed Development of Secondary Sex Characteristics Delayed Onset of Sexual Maturity Delayed Pubertal Development Delayed Sexual Maturation Delayed Sexual Maturity Delayed pubertal growth Pubertal Delay Delayed Puberty HP:0000824 Insufficient production of growth hormone, which is produced by the anterior pituitary gland. Growth hormone is a major participant in control of growth and metabolism. Sufficient SCDO:0008218 HP:0000824 Growth Hormone Deficiency HP:0000828 An abnormality of the parathyroid gland. Sufficient SCDO:1000279 HP:0000828 Abnormality of the Parathyroid Gland HP:0000829 A condition caused by a deficiency of parathyroid hormone characterized by hypocalcemia and hyperphosphatemia. Sufficient SCDO:0007386 HP:0000829 Decreased Parathyroid Hormone Secretion Low Parathyroid Hormone Hypoparathyroidism HP:0000834 Abnormality of the adrenal glands, i.e., of the endocrine glands located at the top of the kidneys. Sufficient SCDO:0007437 HP:0000834 Adrenal Abnormalities Adrenal Abnormality Abnormality of the Adrenal Glands HP:0000836 An abnormality of thyroid physiology characterized by excessive secretion of the thyroid hormones thyroxine (i.e., T4) and/or 3,3',5-triiodo-L-thyronine zwitterion (i.e., triiodothyronine or T3). Provide source for additional info. http://purl.obolibrary.org/obo/HP_0000836 Sufficient SCDO:0000595 HP:0000836 Overactive Thyroid Hyperthyroidism HP:0000842 An increased concentration of insulin in the blood. Provide source for additional info. http://purl.obolibrary.org/obo/HP_0000842 Sufficient SCDO:0000587 HP:0000842 Elevated Insulin Level Hyperinsulinemia HP:0000843 Excessive production of parathyroid hormone (PTH) by the parathyroid glands. Provide source for additional info. http://purl.obolibrary.org/obo/HP_0000843 Sufficient SCDO:0000592 HP:0000843 Elevated Blood Parathyroid Hormone Level Hyperparathyroidism HP:0000855 Increased resistance towards insulin, that is, diminished effectiveness of insulin in reducing blood glucose levels. http://purl.obolibrary.org/obo/HP_0000855 Sufficient SCDO:0000644 HP:0000855 Body Fails to Respond to Insulin Insulin Resistance HP:0000873 A state of excessive water excretion and hypotonic (dilute) polyuria. Diabetes insipidus may be due to failure of vasopressin (AVP) release (central or neurogenic diabetes insipidus) or to a failure of the kidney to respond to AVP (nephrogenic diabetes insipidus). http://purl.obolibrary.org/obo/HP_0000873 Sufficient SCDO:0000366 HP:0000873 Diabetes Insipidus HP:0000876 Infrequent menses (less than 6 per year or more than 35 days between cycles). Sufficient SCDO:0003158 HP:0000876 Light or Infrequent Menstrual Periods Oligomenorrhea HP:0000924 An abnormality of the skeletal system. Sufficient SCDO:0006301 HP:0000924 Skeletal Abnormalities Skeletal Anomalies Abnormality of the Skeletal System HP:0000938 Osteopenia is a term to define bone density that is not normal but also not as low as osteoporosis. By definition from the World Health Organization osteopenia is defined by bone densitometry as a T score -1 to -2.5. Provide source for additional info. http://purl.obolibrary.org/obo/HP_0000938 Sufficient SCDO:0000843 HP:0000938 Decreased Bone Mineral Density Generalized Osteopenia Osteopenia HP:0000939 Osteoporosis is a systemic skeletal disease characterized by low bone density and microarchitectural deterioration of bone tissue with a consequent increase in bone fragility. According to the WHO criteria, osteoporosis is defined as a BMD that lies 2.5 standard deviations or more below the average value for young healthy adults (a T-score below -2.5 SD). Provide source for additional info. http://purl.obolibrary.org/obo/HP_0000939 Genetic predisposition, low calcium diet, getting little exercise, smoking, decrease in estrogen at the menopause, steroid medicine use for a long time, Vitamin D insufficiency. Bone pain, backache, gradual loss of height, stooped posture, fractures. Sufficient SCDO:0000844 HP:0000939 Osteoporosis HP:0000951 An abnormality of the skin. http://purl.obolibrary.org/obo/HP_0000951 Sufficient SCDO:0008348 HP:0000951 Abnormal skin morphology Abnormal skin structure Dermatopathy Dermopathy Skin Abnormality Abnormality of the Skin HP:0000952 Yellow pigmentation of the skin or sclera due to bilirubin, which in turn is the result of increased bilirubin concentration in the bloodstream. http://purl.obolibrary.org/obo/HP_0000952 Sufficient SCDO:0000671 HP:0000952 Icterus Yellow Skin Yellowing of the Skin Jaundice HP:0000953 A darkening of the skin related to an increase in melanin production and deposition. http://purl.obolibrary.org/obo/HP_0000953 Sufficient SCDO:0000308 HP:0000953 Hyperpigmentation of the Skin Increased Skin Pigmentation Melanoderma Melanodermia Skin Hyperpigmentation Cutaneous Hyperpigmentation HP:0000961 Bluish discoloration of the skin and mucosa due to poor circulation or inadequate oxygenation of arterial or capillary blood. Sufficient SCDO:0000309 HP:0000961 Blue Discoloration of the Skin Cyanotic Cyanosis HP:0000962 Hyperkeratosis is thickening of the outer layer of the skin, the stratum corneum, which is composed of large, polyhedral, plate-like envelopes filled with keratin which are the dead cells that have migrated up from the stratum granulosum. Sufficient SCDO:0000589 HP:0000962 Hyperkeratosis HP:0000967 Petechiae are pinpoint-sized reddish/purple spots, resembling a rash, that appear just under the skin or a mucous membrane when capillaries have ruptured and some superficial bleeding into the skin has happened. This term refers to an abnormally increased susceptibility to developing petechiae. Sufficient SCDO:0000892 HP:0000967 Petechiae HP:0000969 An abnormal accumulation of fluid beneath the skin, or in one or more cavities of the body. http://purl.obolibrary.org/obo/HP_0000969 Sufficient SCDO:0000823 HP:0000969 Dropsy Fluid Retention Hydrops Oedema Water Retention Edema HP:0000980 Abnormally pale skin. Sufficient SCDO:0000863 HP:0000980 Pallor HP:0000999 Any manifestation of a skin disease associated with the production of pus. Sufficient SCDO:0000946 HP:0000999 Pus-Filled Lesion Pyoderma HP:0001010 A reduction of skin color related to a decrease in melanin production and deposition. Sufficient SCDO:0000601 HP:0001010 Hypopigmentation of the Skin Hypopigmented Skin Skin Hypopigmentation Hypopigmentation HP:0001022 An abnormal reduction in the amount of pigmentation (reduced or absent) of skin, hair and eye (iris and retina). Sufficient SCDO:0000036 HP:0001022 Achromasia Albinism HP:0001025 Raised, well-circumscribed areas of erythema and edema involving the dermis and epidermis. Urticaria is intensely pruritic, and blanches completely with pressure. Sufficient SCDO:0001219 HP:0001025 Hives Urticaria HP:0001061 A skin condition in which there is an increase in sebum secretion by the pilosebaceous apparatus associated with open comedones (blackheads), closed comedones (whiteheads), and pustular nodules (papules, pustules, and cysts). Sufficient SCDO:0000012 HP:0001061 Break Out Breaking Out Acne HP:0001081 Hard, pebble-like deposits that form within the gallbladder. Add here "bilirubin gallstones" (see paper "Liver involvement in sickle cell disease" by Emel GÜRKAN et al.). in HP these are called "Pigment Gallstones". http://purl.obolibrary.org/obo/HP_0001081 Sufficient SCDO:0007091 HP:0001081 Gallstones Cholelithiasis HP:0001197 An abnormality of the fetus or the birth of the fetus, excluding structural abnormalities. Sufficient SCDO:1000262 HP:0001197 Abnormality of Prenatal Development or Birth HP:0001250 Seizures are an intermittent abnormality of the central nervous system due to a sudden, excessive, disorderly discharge of cerebral neurons and characterized clinically by some combination of disturbance of sensation, loss of consciousness, impairment of psychic function, or convulsive movements. The term epilepsy is used to describe chronic, recurrent seizures. Provide source for additional info. http://purl.obolibrary.org/obo/HP_0001250 Sufficient SCDO:0001030 HP:0001250 Seizures Seizure HP:0001254 A state of disinterestedness, listlessness, and indifference, resulting in difficulty performing simple tasks or concentrating. Sufficient SCDO:0003089 HP:0001254 Lethargy HP:0001260 Dysarthric speech is a general description referring to a neurological speech disorder characterized by poor articulation. Depending on the involved neurological structures, dysarthria may be further classified as spastic, flaccid, ataxic, hyperkinetic and hypokinetic, or mixed. - Use description to add sub-classes of types of Dysarthria? -- Use text in comments to add relevant terms regarding disease progression? And link to these terms with relevant object property Sufficient SCDO:0000403 HP:0001260 Difficulty Articulating Speech Dysarthric Speech Dysarthria HP:0001265 Reduction of neurologic reflexes such as the knee-jerk reaction. Sufficient SCDO:0000602 HP:0001265 Decreased Reflex Response Decreased Reflexes Hyporeflexia HP:0001269 Loss of strength in the arm, leg, and sometimes face on one side of the body. Hemiplegia refers to a complete loss of strength, whereas hemiparesis refers to an incomplete loss of strength. http://purl.obolibrary.org/obo/HP_0001269 Sufficient SCDO:0008272 HP:0001269 Weakness of One Side of Body Hemiparesis HP:0001271 A generalized disorder of peripheral nerves. http://purl.obolibrary.org/obo/HP_0001271 Acute polyneuropathy has many causes: Infections involving a toxin produced by bacteria, as occurs in diphtheria,An autoimmune reaction (when the body attacks its own tissues), as occurs in Guillain-Barré syndrome (see Guillain-Barré Syndrome), Drugs, including the anticonvulsant phenytoin, some antibiotics (such as chloramphenicol, nitrofurantoin, and sulfonamides), some chemotherapy drugs (such as vinblastine and vincristine), and some sedatives (such as barbital and hexobarbital), Cancer (such as multiple myeloma), which damages nerves by directly invading or putting pressure on them or by triggering an autoimmune reaction, Certain toxins, such as organophosphate insecticides, triorthocresyl phosphate (TOCP), and thallium The cause of chronic polyneuropathy is often unknown. Known causes include the following: Diabetes Mellitus, Excessive use of alcohol, Nutritional deficiencies (such as thiamin deficiency), an uncommon cause in the United States, except among alcoholics who are malnourished, Vitamin B12 deficiency, which causes subacute combined degeneration of the spinal cord (see Subacute Combined Degeneration) and often pernicious anemia (see Inadequate absorption), An underactive thyroid gland (hypothyroidism), Toxic substances, including heavy metals such as lead and mercury, Kidney failure, Certain cancers, such as lung cancer, Rarely, vitamin B6 (pyridoxine) taken in excessive amounts. Acute polyneuropathy (as occurs in Guillain-Barré syndrome) begins suddenly in both legs and progresses rapidly upward to the arms. Symptoms include weakness and a pins-and-needles sensation or loss of sensation. The muscles that control breathing may be affected, resulting in respiratory failure.In the most common form of chronic polyneuropathy, only sensation is affected. Usually, the feet are affected first, but sometimes the hands are. A pins-and-needles sensation, numbness, burning pain, and loss of vibration sense and position sense (knowing where the arms and legs are) are prominent symptoms. Because position sense is lost, walking and even standing become unsteady. Consequently, muscles may not be used. Eventually, they may weaken and waste away. Then, muscles may become stiff and permanently shortened (called contractures). Diabetic neuropathy commonly causes painful tingling or burning sensations in the hands and feet-a condition called distal polyneuropathy. Pain is often worse at night and may be aggravated by touch or by a change in temperature. People may lose the senses of temperature and pain, so they often burn themselves and may have open sores caused by prolonged pressure or other injuries. Without pain as a warning of too much stress, joints are susceptible to injuries. This type of injury is called neurogenic arthropathy (Charcot joints) Polyneuropathy often affects the nerves of the autonomic nervous system, which controls involuntary functions in the body (such as blood pressure, heart rate, digestion, salivation, and urination). Typical symptoms are constipation, sexual dysfunction, and fluctuating blood pressure-most notably a sudden fall in blood pressure when a person stands up (orthostatic hypotension). The skin may become pale and dry, and sweating may be reduced. Much less often, control of bowel movements or urination is lost, leading to fecal or urinary incontinence. Sufficient SCDO:0000914 HP:0001271 Peripheral Nerve Disease Polyneuropathy HP:0001279 Syncope refers to a generalized weakness of muscles with loss of postural tone, inability to stand upright, and loss of consciousness. Once the patient is in a horizontal position, blood flow to the brain is no longer hindered by gravitation and consciousness is regained. Unconsciousness usually lasts for seconds to minutes. Headache and drowsiness (which usually follow seizures) do not follow a syncopal attack. Syncope results from a sudden impairment of brain metabolism usually due to a reduction in cerebral blood flow. http://purl.obolibrary.org/obo/HP_0001279 Sufficient SCDO:0008553 HP:0001279 Fainting Spell Syncope HP:0001287 Inflammation of the meninges. Sufficient SCDO:0000744 HP:0001287 Meningitis HP:0001289 Lack of clarity and coherence of thought, perception, understanding, or action. -- Perhaps move below "Behavioral Abnormality"? Sufficient SCDO:0000273 HP:0001289 Confusion HP:0001298 A term that means brain disease, damage, or malfunction. In general, it is manifested by an altered mental state. -- Provide source for additional info. -- -- Specify which Blood Tests and Which Imaging Tests are used to diagnose. Sufficient SCDO:0000429 HP:0001298 Encephalopathy HP:0001342 Hemorrhage into the parenchyma of the brain. http://purl.obolibrary.org/obo/HP_0001342 Sufficient SCDO:0000209 HP:0001342 Bleeding in Brain Hemorrhagic Stroke Intracerebral Bleeding Intracerebral Hemorrhage Cerebral Hemorrhage HP:0001343 Damage to cerebral nuclei caused in infants by highly increased levels of unconjugated bilirubin. The basal ganglia and brainstem nuclei could be shown to have a yellow staining historically in infants who died of kernicterus, that is, kernicterus is strictly speaking a pathological diagnosis. The presence of kernicterus may be inferred in infants with characteristic acute or chronic bilirubin-induced neurological dysfunction. Sufficient SCDO:0000673 HP:0001343 Kernicterus HP:0001369 Inflammation of a joint. http://purl.obolibrary.org/obo/HP_0001369 Any age Infection (bacteria), ischemia, joint injury (trauma, surgery), degeneration. Joint pain, joint swelling, stiffness, lack of function. Sufficient SCDO:0000075 HP:0001369 Joint Inflammation Arthritis HP:0001370 An autoimmune response that primarily affects connective tissue; it also results in chronic inflammation of the joints, especially of the hands and feet and may also cause inflammation of the tissue around the joints, as well as other organs in the body. Provide source for additional info. http://purl.obolibrary.org/obo/MP_0003561 Sufficient SCDO:0001011 HP:0001370 Osteoarthrosis Deformans RA Rheumatoid Arthritis HP:0001371 A flexion contracture is a bent (flexed) joint that cannot be straightened actively or passively. It is thus a chronic loss of joint motion due to structural changes in muscle, tendons, ligaments, or skin that prevents normal movement of joints. http://purl.obolibrary.org/obo/HP_0001371 Sufficient SCDO:0001324 HP:0001371 Flexion Contractures Flexion Contractures of Joints Joint Contracture Joint Contractures Flexion Contracture HP:0001382 The ability of a joint to move beyond its normal range of motion. Provide source for additional info. http://purl.obolibrary.org/obo/HP_0001382 Sufficient SCDO:0000672 HP:0001382 Double-Jointed Hyperextensible Joints Increased Mobility of Joints Joint Hyperextensibility Joint Hypermobility HP:0001392 An abnormality of the liver. Sufficient SCDO:1000272 HP:0001392 Complication of the Liver Liver Abnormality Liver Complication Abnormality of the Liver HP:0001394 A chronic disorder of the liver in which liver tissue becomes scarred and is partially replaced by regenerative nodules and fibrotic tissue resulting in loss of liver function. Sufficient SCDO:0001488 HP:0001394 Hepatic Cirrhosis Scar Tissue Replaces Healthy Tissue in the Liver Cirrhosis HP:0001395 The presence of excessive fibrous connective tissue in the liver. Fibrosis is a reparative or reactive process. Sufficient SCDO:0001493 HP:0001395 Hepatic Fibrosis HP:0001406 Impairment of bile flow due to obstruction in the small bile ducts within the liver. Is managed by: analgesia, hydration, antibiotics, and in severe cases exchange transfusion may be needed. http://purl.obolibrary.org/obo/HP_0001406 Sufficient SCDO:0009774 HP:0001406 Intrahepatic Cholestasis HP:0001433 Simultaneous enlargement of the liver and spleen. Sufficient SCDO:0007326 HP:0001433 Hepatosplenomegaly HP:0001507 Abnormality of growth. Sufficient SCDO:1000271 HP:0001507 Abnormal Growth Growth Issue Growth Abnormality HP:0001508 Failure to thrive (FTT) refers to a child whose physical growth is substantially below the norm. Sufficient SCDO:0002729 HP:0001508 FTT Faltering Weight Poor Weight Gain Postnatal Failure to Thrive Undergrowth Weight Faltering Failure to Thrive HP:0001511 An abnormal restriction of fetal growth with fetal weight below the tenth percentile for gestational age. Provide source for additional info. http://purl.obolibrary.org/obo/HP_0001511 Sufficient SCDO:0000658 HP:0001511 IUGR Intrauterine Growth Retardation Prenatal Growth Retardation Prenatal-Onset Growth Retardation Small for Gestational Age Infant Intrauterine Growth Restriction HP:0001513 Body weight that is grossly above the acceptable or desirable weight, usually due to accumulation of excess fats in the body. The standards may vary with age, sex, genetic or cultural background. In the body mass index (BMI), a BMI greater than 30.0 kg/m2 is considered obese, and a BMI greater than 40.0 kg/m2 is considered morbidly obese. http://purl.obolibrary.org/obo/HP_0001513 Sufficient SCDO:0000816 HP:0001513 Having too much body fat Obesity HP:0001574 An abnormality of the integument, which consists of the skin and the superficial fascia. Sufficient SCDO:1000274 HP:0001574 Abnormality of the Integument HP:0001622 The birth of a baby of less than 37 weeks of gestational age. Provide source for additional info. http://purl.obolibrary.org/obo/HP_0001622 Sufficient SCDO:0000920 HP:0001622 Premature Birth Premature Delivery Premature Delivery of Affected Infants Preterm Birth Preterm Delivery HP:0001626 Any abnormality of the cardiovascular system. http://purl.obolibrary.org/obo/HP_0001626 Sufficient SCDO:0002245 HP:0001626 Abnormality of the Cardiovascular System Cardiovascular Abnormality Abnormality of Cardiovascular System HP:0001635 The presence of an abnormality of cardiac function that is responsible for the failure of the heart to pump blood at a rate that is commensurate with the needs of the tissues or a state in which abnormally elevated filling pressures are required for the heart to do so. Heart failure is frequently related to a defect in myocardial contraction. Sufficient SCDO:0004877 HP:0001635 CHF Cardiac Insufficiency, Congestive Heart Failure Heart Failure Cardiac Failure HP:0001640 Increased size of the heart. http://purl.obolibrary.org/obo/HP_0001640 Sufficient SCDO:0008273 HP:0001640 Enlarged Heart Increased Heart Size Cardiomegaly HP:0001658 Necrosis of the myocardium caused by an obstruction of the blood supply to the heart and often associated with chest pain, shortness of breath, palpitations, and anxiety as well as characteristic EKG findings and elevation of serum markers including creatine kinase-MB fraction and troponin. http://purl.obolibrary.org/obo/HP_0001658 Sufficient SCDO:0007991 HP:0001658 Myocardial Infarction HP:0001701 Inflammation of the sac-like covering around the heart (pericardium). Sufficient SCDO:0003765 HP:0001701 Pericarditis HP:0001712 Enlargement or increased size of the heart left ventricle. Sufficient SCDO:0002803 HP:0001712 Heart Left Ventricle Hypertrophy Left Ventricular Wall Hypertrophy Left Ventricular Hypertrophy HP:0001714 Enlargement of the cardiovascular ventricular muscle tissue with increase in the width of the wall of the ventricle and loss of elasticity. Ventricular hypertrophy is clinically differentiated into left and right ventricular hypertrophy. http://purl.obolibrary.org/obo/HP_0001714 Sufficient SCDO:0001231 HP:0001714 Ventricular Hypertrophy HP:0001743 An abnormality of the spleen. Sufficient SCDO:1000370 HP:0001743 Abnormality of the Spleen HP:0001744 Abnormal increased size of the spleen. http://purl.obolibrary.org/obo/HP_0001744 Sufficient SCDO:0005287 HP:0001744 Increased Spleen Size Results from splenic sequestration Splenomegaly HP:0001787 An abnormality of the birth process. Sufficient SCDO:1000372 HP:0001787 Abnormal Delivery HP:0001789 The abnormal accumulation of fluid in two or more fetal compartments, including ascites, pleural effusion, pericardial effusion, and skin edema. http://purl.obolibrary.org/obo/HP_0001789 Sufficient SCDO:0000578 HP:0001789 Hydrops Fetalis HP:0001871 An abnormality of the hematopoietic system. Sufficient SCDO:1000264 HP:0001871 Abnormality of the Hematopoietic System Hematological Abnormality Hematopoietic System Abnormality Abnormality of Blood and Blood-Forming Tissues HP:0001872 An abnormality of platelets. Platelets, also known as thrombocytes, are non-nucleated disk-shaped cells mainly involved in blood coagulation. Sufficient SCDO:1000616 HP:0001872 Platelet Abnormalities Abnormal Thrombocyte Morphology HP:0001873 A reduction in the number of circulating thrombocytes. Sufficient SCDO:0002700 HP:0001873 Thrombocytopenia HP:0001874 A neutrophil abnormality. Sufficient SCDO:1000440 HP:0001874 Neutrophils are the most abundant leukocytes in blood and are considered to be the first line of defense during inflammation and infections. They are myeloid granulocytes and their names is derived from the fact that their cytoplasm contains granules that stain with acidic dye as well as granules that stain with basic dye. Their nuclei consist of three to five lobes connected by slender threads of chromatin. Mature neutrophils live for approximately one day. Abnormality of Neutrophils HP:0001875 An abnormally low number of neutrophils in the peripheral blood. Sufficient SCDO:0009334 HP:0001875 Decreased Neutrophil Count Low Blood Neutrophil Count Low Neutrophil Count Peripheral Neutropenia Neutropenia HP:0001877 Any structural abnormality of erythrocytes (red-blood cells). Sufficient SCDO:1000285 HP:0001877 Abnormal Erythrocyte Morphology HP:0001878 A type of anemia caused by premature destruction of red blood cells (hemolysis). http://purl.obolibrary.org/obo/HP_0001878 Sufficient SCDO:0003844 HP:0001878 Hemolytic Anemia HP:0001882 An abnormal decreased number of leukocytes in the blood. Sufficient SCDO:1000614 HP:0001882 Decreased Blood Leukocyte Number Low White Blood Cell Count Leukopenia HP:0001889 Anemia characterized by the presence of erythroblasts that are larger than normal (megaloblasts). http://purl.obolibrary.org/obo/HP_0001889 Sufficient SCDO:0005864 HP:0001889 Megaloblastic Anemia HP:0001894 Thrombocythemia and thrombocytosis are conditions with a higher than normal number of platelets. The term "thrombocythemia" is preferred when the cause of a high platelet count isn't known. The condition sometimes is called primary or essential thrombocythemia. Increased numbers of platelets in the peripheral blood. Sufficient SCDO:1000618 HP:0001894 Increased Number of Platelets in Blood Increased Platelet Count Thrombocytosis HP:0001896 A reduced number of reticulocytes in the peripheral blood. Sufficient SCDO:0001423 HP:0001896 Low Reticulocyte Count Reduced Number of Reticulocytes Reduced Reticulocyte Count Reticulocytopenia HP:0001903 A reduction in erythrocytes volume or hemoglobin concentration. http://purl.obolibrary.org/obo/HP_0001903 Sufficient SCDO:0005660 HP:0001903 Anemia HP:0001909 A cancer of the blood and bone marrow characterized by an abnormal proliferation of leukocytes. http://purl.obolibrary.org/obo/HP_0001909 Sufficient SCDO:0000687 HP:0001909 Blood Cancer Leukaemia HP:0001919 Sudden loss of renal function, as manifested by decreased urine production, and a rise in serum creatinine or blood urea nitrogen concentration (azotemia). Further work Provide source for additional info. There is conflicting positioning of this term in different ontologies. Need an expert to decide descriptions and positioning of this and related terms. http://purl.obolibrary.org/obo/HP_0001919 Sufficient SCDO:0000017 HP:0001919 Acute Kidney Failure Acute Renal Failure Acute renal failure is usually classified into prerenal (response to severe volume depletion), intrinsic (response to acute cytotoxic, ischemic, or inflammatory insults) and postrenal (response to obstruction of the passage of urine) etiologies. Acute Kidney Injury HP:0001920 The presence of stenosis of the renal artery. Provide source for additional info. If due to FMD, presents at younger age, typically between 25-50 (and more common in women); if related to atherosclerotic disase, more likely to present after age 50. May be caused by atherosclerotic disease, fibromuscular dysplasia. Reduced blood flow through the renal arteries, large and branching vessels. Sufficient SCDO:0000982 HP:0001920 Narrowing of Kidney Artery RAS Renal Artery Stenosis HP:0001923 An elevation in the number of reticulocytes (immature erythrocytes) in the peripheral blood circulation. Sufficient SCDO:0001272 HP:0001923 High Reticulocyte Count Increased Immature Red Blood Cells Increased Number of Immature Red Blood Cells Increased Reticulocyte Count Increased Reticulocytes Reticulocytosis HP:0001931 A type of anemia characterized by an abnormally low concentration of hemoglobin in the erythrocytes. Sufficient SCDO:0007371 HP:0001931 Hypochromic Anemia HP:0001935 A kind of anemia in which the volume of the red blood cells is reduced. Sufficient SCDO:0008538 HP:0001935 In normocytic anemia, the mean corpuscular volume (MCV) is below normal limits (>80 fl in adults). Microcytic Anemia HP:0001943 A decreased concentration of glucose in the blood. Provide source for additional info. http://purl.obolibrary.org/obo/HP_0001943 Sufficient SCDO:0000599 HP:0001943 Low Blood Sugar Hypoglycemia HP:0001953 A type of diabetic metabolic abnormality with an accumulation of ketone bodies. http://purl.obolibrary.org/obo/HP_0001953 Sufficient SCDO:0000369 HP:0001953 Diabetic Ketosis Diabetic Ketoacidosis HP:0001970 A form of inflammation of the kidney affecting the interstitium of the kidneys surrounding the tubules. Sufficient SCDO:0000652 HP:0001970 Tubulointerstitial Nephritis Interstitial Nephritis HP:0001974 An abnormal increase in the number of leukocytes in the blood. Sufficient SCDO:0005790 HP:0001974 Elevated White Blood Count High White Blood Count Increased Blood Leukocyte Number Leukocytosis HP:0001977 Venous or arterial thrombosis (formation of blood clots) of spontaneous nature and which cannot be fully explained by acquired risk (e.g. atherosclerosis). Sufficient SCDO:1000287 HP:0001977 Abnormal Thrombosis HP:0001999 An abnormal morphology (form) of the face or its components. Provide source for additional info. http://purl.obolibrary.org/obo/HP_0001999 Sufficient SCDO:0001314 HP:0001999 Abnormal Morphology of the Face Abnormal facial shape Dysmorphic Facial Features Unusual Facial Appearance Facial Dysmorphisms HP:0002007 Bilateral bulging of the lateral frontal bone prominences with relative sparing of the midline. http://purl.obolibrary.org/obo/HP_0002007 Sufficient SCDO:0001337 HP:0002007 Frontal Protruberance Skull Bossing Frontal Bossing HP:0002014 Abnormally increased frequency of loose or watery bowel movements. Sufficient SCDO:0008043 HP:0002014 Diarrhoea Watery stool Diarrhea HP:0002019 Infrequent or difficult evacuation of feces. http://purl.obolibrary.org/obo/HP_0002019 Sufficient SCDO:0003263 HP:0002019 Constipation Costiveness Dyschezia Constipation HP:0002059 Atrophy (wasting, decrease in size of cells or tissue) affecting the cerebrum. http://purl.obolibrary.org/obo/HP_0002059 Sufficient SCDO:0000203 HP:0002059 Cortical Atrophy Degeneration of Cerebrum Supratentorial Atrophy Atrophy may be progressive over time. Cerebral Atrophy HP:0002060 An abnormality of the telencephalon, which is also known as the cerebrum. http://purl.obolibrary.org/obo/HP_0002060 Sufficient SCDO:0008895 HP:0002060 Abnormal Cerebral Morphology Abnormality of the Telencephalon Abnormality of the Cerebrum HP:0002067 Bradykinesia literally means slow movement, and is used clinically to denote a slowness in the execution of movement (in contrast to hypokinesia, which is used to refer to slowness in the initiation of movement). http://purl.obolibrary.org/obo/HP_0002067 Sufficient SCDO:0000158 HP:0002067 Slow Movements Slowness of Movements Bradykinesia HP:0002071 A neurological condition related to lesions of the basal ganglia leading to typical abnormalities including akinesia (inability to initiate changes in activity and perform volitional movements rapidly and easily), muscular rigidity (continuous contraction of muscles with constant resistance to passive movement), chorea (widespread arrhythmic movements of a forcible, rapid, jerky, and restless nature), athetosis (inability to sustain the muscles of the fingers, toes, or other group of muscles in a fixed position), and akathisia (inability to remain motionless). Sufficient SCDO:0001311 HP:0002071 Abnormality of Extrapyramidal Motor Function Extrapyramidal Dysfunction Extrapyramidal Signs Extrapyramidal Syndrome Extrapyramidal Tract Signs Extrapyramidal Symptoms HP:0002076 Migraine is a chronic neurological disorder characterized by episodic attacks of headache and associated symptoms. Sufficient SCDO:0000759 HP:0002076 Intermittent Migraine Headaches Migraine Headache Roughly one-third of affected individuals can predict the onset of a migraine because it is preceded by an "aura," visual disturbances that appear as flashing lights, zig-zag lines or a temporary loss of vision. People with migraine tend to have recurring attacks triggered by a number of different factors, including stress, anxiety, hormonal changes, bright or flashing lights, lack of food or sleep, and dietary substances. Migraine in some women may relate to changes in hormones and hormonal levels during their menstrual cycle. For many years, scientists believed that migraines were linked to the dilation and constriction of blood vessels in the head. Investigators now believe that migraine has a genetic cause. Migraine HP:0002086 An abnormality of the respiratory system, which include the airways, lungs, and the respiratory muscles. Curation completed by the SCDO curator team: Amy and Khuthala. http://purl.obolibrary.org/obo/HP_0002086 Sufficient SCDO:0004899 HP:0002086 Respiratory Abnormality Abnormality of the Respiratory System HP:0002090 Inflammation of any part of the lung parenchyma. Sufficient SCDO:0009838 HP:0002090 Pneumonia HP:0002098 Difficulty in breathing. The physical presentation of respiratory distress is generally referred to as labored breathing, while the sensation of respiratory distress is called shortness of breath or dyspnea. Is a symptom of acute chest syndrome http://purl.obolibrary.org/obo/HP_0002098 Sufficient SCDO:0009656 HP:0002098 Breathing Difficulties Difficulty Breathing Respiratory Difficulties Respiratory Distress HP:0002138 Hemorrhage occurring between the arachnoid mater and the pia mater. Sufficient SCDO:0001118 HP:0002138 Subarachnoid Haemorrhage Subarachnoid hemorrhage may occur spontaneously, usually from a ruptured cerebral aneurysm, or may result from head injury. Subarachnoid Hemorrhage HP:0002149 An abnormally high level of uric acid in the blood. Sufficient SCDO:0000596 HP:0002149 High Blood Uric Acid Level Hyperuricaemia Hyperuricemia HP:0002157 An increased concentration of nitrogen compounds in the blood. Perhaps move to below "Endocrine and Metabolic"? -- -- Check and show which source was used for the description and whether the description was adapted from the source. -- Provide source for additional info. Sufficient SCDO:0000093 HP:0002157 Azotemia Azotaemia HP:0002164 The presence of developmental dysplasia of the nail. Sufficient SCDO:0000830 HP:0002164 Dysplastic Nails Onychodysplasia Nail Dysplasia HP:0002170 Hemorrhage occurring within the skull. Sufficient SCDO:0000654 HP:0002170 Intracranial Hemorrhage HP:0002181 Abnormal accumulation of fluid in the brain. Provide source for additional info. http://purl.obolibrary.org/obo/HP_0002181 Sufficient SCDO:0000207 HP:0002181 Brain Edema Brain Oedema Cerebral Oedema Cerebral Edema HP:0002204 An embolus (that is, an abnormal particle circulating in the blood) located in the pulmonary artery and thereby blocking blood circulation to the lung. Usually the embolus is a blood clot that has developed in an extremity (for instance, a deep venous thrombosis), detached, and traveled through the circulation before becoming trapped in the pulmonary artery. Sufficient SCDO:0007912 HP:0002204 Blood Clot in Artery of Lung Pulmonary Embolism HP:0002240 Abnormally increased size of the liver. Sufficient SCDO:0005566 HP:0002240 Hepatomegaly HP:0002341 Compression of the spinal cord in the cervical region, generally manifested by paresthesias and numbness, weakness, difficulty walking, abnormalities of coordination, and neck pain or stiffness. http://purl.obolibrary.org/obo/HP_0002341 Sufficient SCDO:0000214 HP:0002341 Cervical Cord Compression Myelopathy Cervical Spondylotic Myelopathy Spinal Cord Compression Cervical Cord Compression HP:0002427 Impairment of expressive language and relative preservation of receptive language abilities. That is, the patient understands language (speech, writing) but cannot express it. Aphasia is one of the most common communication disorders to affect the brain. Although there are no official figures, the Stroke Association estimates more than 376,000 stroke survivors in the UK are living with aphasia. Aphasia can affect people of all ages, including children. It's most common in people over 65 years old as stroke and common progressive neurological conditions tend to affect older adults Aphasia is caused by damage to parts of the brain responsible for understanding and using language. Common causes include:stroke, thought to be the most common cause, around one in three people experience some degree of aphasia after having a stroke.severe head injury. brain tumour.progressive neurological conditions (conditions that over time cause progressive brain and nervous system damage). Experience difficulties with understanding or expressing language. Sufficient SCDO:0000773 HP:0002427 Broca's Aphasia Expressive Aphasia Loss of Expressive Speech Motor Aphasia HP:0002516 An increase of the pressure inside the cranium (skull) and thereby in the brain tissue and cerebrospinal fluid. http://purl.obolibrary.org/obo/HP_0002516 Sufficient SCDO:0000655 HP:0002516 Increased Intracranial Pressure Intracranial Pressure Elevation Rise in Pressure Inside Skull Intracranial Hypertension HP:0002597 An abnormality of the vasculature. Sufficient SCDO:1000373 HP:0002597 Abnormality of the Vasculature HP:0002650 The presence of an abnormal lateral curvature of the spine. Provide source for additional info. http://purl.obolibrary.org/obo/HP_0002650 Congenital vertebral anomalies, idiopathic, result of a neuromuscular condition. Spinal tortuosity. Sufficient SCDO:0001026 HP:0002650 Abnormal Curving of the Spine Scoliosis HP:0002653 An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) localized to bone. Provide source for additional info. http://purl.obolibrary.org/obo/HP_0002653 A number of diseases may cause bone pain including osteoarthritis, Paget's disease, sickle cell anemia, and bone cancer. Acute leukemia;Acute rheumatic fever, a very dangerous disease that can cause permanent cardiac damage. Bursitis;Fibromyalgia like disease has been studied as a cause of joint pain in the child.Hypermobility syndrome can present with knee or ankle pain;Injury such as a fracture. Juvenile rheumatoid arthritis;Lupus;Lyme disease, which is transmitted by ticks and is characterized by debilatating polyarthritis, neurologic symptoms, and erythema migrans.;Osteomyelitis;Osteosarcoma.Septic arthritis, a severe infection of the joint that can lead to permanent joint damage.Synovitis;Viral diseases, including the measles, influenza, mononucleosis, chickenpox, and mumps. Stimulation of specialized pain-sensitive nerve fibers (nociceptors) that innervate bone tissue leads to the sensation of bone pain. Bone pain originates from both the periosteum and the bone marrow which relay nociceptive signals to the brain creating the sensation of pain. Bone tissue is innervated by both myelinated (A beta and A delta fiber) and unmyelinated (C fiber) sensory neurons. In combination, they can provide an initial burst of pain, initiated by the faster myelinated fibers, followed by a slower and longer lasting dull pain initiated by unmyelinated fibers Sufficient SCDO:0000154 HP:0002653 Bone Pain HP:0002659 An abnormally increased tendency to fractures of bones caused by an abnormal reduction in bone strength that is generally associated with an increased risk of fracture. Provide source for additional info. http://purl.obolibrary.org/obo/HP_0002659 Sufficient SCDO:0000153 HP:0002659 Abnormal Susceptibility to Fractures Frequent Broken Bones Increased Bone Fragility Increased Susceptibility to Fractures Increased Tendency to Fractures Bone Fragility HP:0002665 A cancer originating in lymphocytes and presenting as a solid tumor of lymphoid cells. http://purl.obolibrary.org/obo/HP_0002665 Sufficient SCDO:0000707 HP:0002665 Cancer of Lymphatic System Lymphoma HP:0002715 An abnormality of the immune system. Include as sub-class: Acquired Immunodeficiency Syndrome (term in NCIT) Sufficient SCDO:1000273 HP:0002715 Abnormality of the Immune System HP:0002725 A chronic, relapsing, inflammatory, and often febrile multisystemic disorder of connective tissue, characterized principally by involvement of the skin, joints, kidneys, and serosal membranes. http://purl.obolibrary.org/obo/HP_0002725 Sufficient SCDO:0001137 HP:0002725 Systemic Lupus Erythematosus HP:0002808 Exaggerated anterior convexity of the thoracic vertebral column. http://purl.obolibrary.org/obo/HP_0002808 Sufficient SCDO:0000679 HP:0002808 Gibbus Deformity Hunched Back Hyperkyphosis Round Back Kyphosis HP:0002829 Joint pain. Provide source for additional info. http://purl.obolibrary.org/obo/HP_0002829 Sufficient SCDO:0000074 HP:0002829 Arthralgias Joint pain Arthralgia HP:0002870 A condition characterized by obstruction of the airway and by pauses in breathing during sleep occurring many times during the night. Obstructive sleep apnea is related to a relaxation of muscle tone (which normally occurs during sleep) leading to partial collapse of the soft tissues in the airway with resultant obstruction of the air flow. http://purl.obolibrary.org/obo/HP_0002870 Sufficient SCDO:0000820 HP:0002870 Obstructive Sleep Apnoea Obstructive Sleep Apnea HP:0002907 Microscopic hematuria detected by dipstick or microscopic examination of the urine. http://purl.obolibrary.org/obo/HP_0002907 Sufficient SCDO:0004833 HP:0002907 Microhematuria Occult Hematuria Small Amount of Blood in Urine Microscopic Hematuria HP:0002913 Presence of myoglobin in the urine. Sufficient SCDO:0000783 HP:0002913 Increased Urine Myoglobin Level Myoglobinuria HP:0002955 Any disease characterized by the formation of numerous granulomas. Source needed for additional information. http://purl.obolibrary.org/obo/HP_0002955 Sufficient SCDO:0000464 HP:0002955 Has disease stages: Allergic (Churg-strauss syndrome), eosinophilic (langerhan cell histiocytosis), langerhans (langerhan cell histiocytosis), lymphomatoid, siderotica, wegeners. Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation. Granulomatosis HP:0003077 An elevated lipid concentration in the blood. http://purl.obolibrary.org/obo/HP_0003077 Sufficient SCDO:0000590 HP:0003077 Elevated Lipids in Blood Hyperlipidemia HP:0003110 An abnormality of the composition of urine or the levels of its components. Sufficient SCDO:1000651 HP:0003110 Abnormal Urine Chemistry Abnormality of Urine Homeostasis Abnormal Urine Homeostasis HP:0003116 An abnormality detectable by sonography of the heart (echocardiography). Sufficient SCDO:1000267 HP:0003116 Abnormal ECG Abnormal Echocardiography Abnormal Echocardiogram HP:0003126 Excretion in urine of proteins of a size smaller than albumin (molecular weight 69 kD). http://purl.obolibrary.org/obo/HP_0003126 Sufficient SCDO:0001196 HP:0003126 Low-Molecular-Weight Proteinuria Tubular Proteinuria HP:0003155 Abnormally increased serum levels of alkaline phosphatase activity. Sufficient SCDO:1000664 HP:0003155 Blood Alkaline Phosphatase Increased Decreased Circulating Alkaline Phosphatase Level Elevated ALP Elevated Alkaline Phosphatase High Serum Alkaline Phosphatase Increased Alkaline Phosphatase Reduced Circulating ALP Elevated Serum Alkaline Phosphatase HP:0003158 An abnormally low urinary specific gravity, i.e., reduced concentration of solutes in the urine. Could this be a synonym for 'Impaired Urinary Concentration' (SCDO:0000621)? http://purl.obolibrary.org/obo/HP_0003158 Sufficient SCDO:0008046 HP:0003158 Urine specific gravity is lower than that of plasma < 1.008. Hyposthenuria HP:0003198 A disorder of muscle unrelated to impairment of innervation or neuromuscular junction. Provide source for additional info. http://purl.obolibrary.org/obo/HP_0003198 Sufficient SCDO:0000784 HP:0003198 Muscle Tissue Disease Myopathic Changes Myopathies Myopathy HP:0003265 A type of hyperbilirubinemia with neonatal onset. Sufficient SCDO:0003776 HP:0003265 High Blood Bilirubin Levels in Neonate Neonatal Hyperbilirubinemia HP:0003282 Abnormally reduced serum levels of alkaline phosphatase. Sufficient SCDO:1000667 HP:0003282 Low ALP Low Alkaline Phosphatase Reduced Serum Alkaline Phosphatase Decreased Serum Alkaline Phosphatase HP:0003302 Complete bilateral fractures of the pars interarticularis resulting in the anterior slippage of the vertebra. Provide source for additional info. http://purl.obolibrary.org/obo/HP_0003302 Spondylolysis, arthritis, degeneration, trauma, metastases or metabolic bone disease, congenital. Sufficient SCDO:0001102 HP:0003302 Displacement of One Backbone Compared to Another Slipped Backbone Spondylolithesis Spondylolisthesis HP:0003394 Sudden and involuntary contractions of one or more muscles. Sufficient SCDO:0000778 HP:0003394 Muscle Spasm Muscle Cramps HP:0003418 An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) localized to the back. Provide source for additional info. muscle strain, trauma, surgery, fracture, osteoporosis, fibromialgia, spinal disc herniation. Pain in the lower back. Sufficient SCDO:0000095 HP:0003418 Back Pain HP:0003457 Abnormal results of investigations using electromyography (EMG). Sufficient SCDO:0000428 HP:0003457 Abnormal EMG Abnormal Electromyography (EMG). Abnormal Electromyography Finding EMG Abnormalities Electromyogram Abnormal EMG Abnormality HP:0003470 Paralysis of voluntary muscles means loss of contraction due to interruption of one or more motor pathways from the brain to the muscle fibers. Motor paralysis is often accompanied by an impairment in the facility of movement. Provide source for additional info. http://purl.obolibrary.org/obo/HP_0003470 Most paralysis is due to strokes or injuries such as spinal cord injury or a broken neck. Other causes of paralysis include: Nerve diseases such as amyotrophic lateral sclerosis, Autoimmune diseases such as Guillain-Barre syndrome, Bell's palsy, which affects muscles in the face, Polio used to be a cause of paralysis, but polio no longer occurs in the U.S. Paralysis can be complete or partial. It can occur on one or both sides of your body. It can also occur in just one area, or it can be widespread. Paralysis of the lower half of your body, including both legs, is called paraplegia. Paralysis of the arms and legs is quadriplegia. Sufficient SCDO:0000865 HP:0003470 Inability to Move Paralysis HP:0003563 Reduced amount in the blood of the lipoprotein:cholesterol complex that transports cholesterol out of the arteries and around the body, for use by various tissues in normal bodily functions. Sufficient SCDO:0000703 HP:0003563 Decreased Circulating Low-Density Lipoprotein Levels Decreased LDL Decreased LDL Cholesterol Concentration Decreased LDL Cholesterol Level Decreased LDLc Concentration Low Circulating LDL Cholesterol Level Low LDL-Cholestrol Levels Reduced Circulating LDL Cholesterol Level Decreased Circulating LDL Cholesterol Level HP:0003573 Increased concentration of total (conjugated and unconjugated) bilirubin in the blood. Sufficient SCDO:1000681 HP:0003573 High Bili Total High Total Bilirubin Increased Bilirubin Increased Total Bilirubin HP:0003611 Anomalous concentrations of fat-soluble substances (molecules composed of carbon and hydrogen and are characteristically insoluble in water) in the blood. Provide source for additional info. http://purl.obolibrary.org/obo/MP_0003949 Sufficient SCDO:0000404 HP:0003611 Abnormal Circulating Lipid Concentration Abnormal Circulating Lipid Level Dyslipidaemia Dyslipidemia HP:0003641 The presence of free hemoglobin in the urine. Sufficient SCDO:0000554 HP:0003641 Increased Urine Hemoglobin Level If, following hemolysis, haptoglobins (hemoglobin-binding proteins) are saturated, then free hemoglobin appears in the urine. Hemoglobinuria HP:0003765 A skin abnormality characterized by redness and irritation, with thick, red skin that displays flaky, silver-white patches (scales). Sufficient SCDO:0000936 HP:0003765 Psoriasiform Dermatitis Psoriasis HP:0003774 A degree of kidney failure severe enough to require dialysis or kidney transplantation for survival characterized by a severe reduction in glomerular filtration rate (less than 15 ml/min/1.73 m2) and other manifestations including increased serum creatinine, greater than 3 months. Check and show which source was used for the description and whether the description was adapted from the source. -- Provide source for additional info. Variable Final outcome of any form of kidney disease ; may be caused by diabetes, hypertension, glomerular disease, polycystic kidney disease, sickle cell disease, chronic toxic injury. Elevated serum creatinine, uremia, acidosis, hyperkalemia, hyperphosphatemia, secondary hyperpararthyroidism, anemia, hypertension, fluid retention. Sufficient SCDO:0000430 HP:0003774 ESKD ESRD End Stage Renal Disease End Stage Renal Disease (ESRD) End Stage Renal Failure End-Stage Renal Disease End-Stage Renal Failure Stage 5 Chronic Kidney Disease End Stage Kidney Disease HP:0004312 A reticulocyte abnormality. Sufficient SCDO:1000265 HP:0004312 Abnormality of Reticulocytes HP:0004364 Any deviation from the normal concentration of a nitrogen compound in the blood circulation. Sufficient SCDO:1000647 HP:0004364 Abnormal Circulating Nitrogen Compound Concentration HP:0004379 An abnormality of alkaline phosphatase level. Sufficient SCDO:1000666 HP:0004379 Abnormality Alkaline Phosphatase Level Abnormality of ALP Level Abnormality of Alkaline Phosphatase Activity Alkaline Phosphatase Abnormal Note that the alkaline phosphatase family has four isoenzymes in humans, each of which additionally can have different isoforms. The primary clinical importance of measuring alkaline phosphatase is to check the possibility of bone disease or liver disease. Abnormality of Alkaline Phosphatase Level HP:0004447 The presence of abnormally shaped erythrocytes. Sufficient SCDO:1000245 HP:0004447 Poikilocytosis HP:0004586 Exaggerated concavity of the anterior or posterior surface of the vertebral body, i.e., the upper and lower vertebral endplates are hollowed inward. Sufficient SCDO:0000118 HP:0004586 Biconcave Vertebrae Fish Mouth Deformity Fish Vertebrae Step Vertebrae Biconcave Vertebral Bodies HP:0004727 A defect in the ability to concentrate the urine. http://purl.obolibrary.org/obo/HP_0004727 Notable within the first decade of life. Can be caused by tubular damage in the kidney; can be seen in sickle cell disease and sickle cell trait. Sufficient SCDO:0000621 HP:0004727 UCD Urine Concentrating Defect Urine Concentration Defect Impaired Renal Concentrating Ability HP:0004756 A tachycardia originating in the ventricles characterized by rapid heart rate (over 100 beats per minute) and broad QRS complexes (over 120 ms). Sufficient SCDO:0003769 HP:0004756 VT Ventricular tachycardia (VT) is a potentially life-threatening ventricular arrhythmia that presents as a wide QRS complex tachycardia, and is defined as three or more consecutive QRS complexes with a duration longer than 120 milliseconds (ms) and a rate of 100 beats per minute or more, whereby the complexes have a ventricular origin. VT can be subdivided as follows: (i) sustained VT persists for 30 seconds or more; (ii) non-sustained VT lasts less than 30 seconds; (iii) monomorphic VT displays a uniform QRS morphology; and (iv) polymorphic VT displays QRS morphologies that variy from beat to beat. VT is observed most commonly in individuals with structural heart disease or acute myocardial infarction (MI). VT may also be observed in in the setting of drug toxicity or electrolyte abnormalities or in individuals with Mendelian disease. Ventricular Tachycardia HP:0004825 An abnormal increase in the binding affinity of hemoglobin for oxygen. Sufficient SCDO:1000248 HP:0004825 Increased Haemoglobin Oxygen Affinity Increased Hemoglobin Oxygen Affinity HP:0004870 A chronic form of hemolytic anemia. http://purl.obolibrary.org/obo/HP_0004870 Sufficient SCDO:0001248 HP:0004870 Chronic Hemolytic Anemia HP:0005162 Inability of the left ventricle to perform its normal physiologic function. Failure is either due to an inability to contract the left ventricle or the inability to relax completely and fill with blood during diastole. http://purl.obolibrary.org/obo/HP_0005162 Sufficient SCDO:0002710 HP:0005162 Impaired Left Ventricular Function Left Ventricular Failure Left Ventricular Impairment Left-Sided Heart Failure Left Ventricular Dysfunction HP:0005268 A pregnancy that ends at a stage in which the fetus is incapable of surviving on its own, defined as the spontaneous loss of a fetus before the 20th week of pregnancy. Sufficient SCDO:0001103 HP:0005268 Miscarriage Spontaneous Abortion HP:0005305 Formation of a blood clot (thrombus) inside a cerebral vein, causing the obstruction of blood flow. Add "Cerebral Venous Sinus Thrombosis" (in the Stroke Ontology) as a sub-class http://purl.obolibrary.org/obo/HP_0005305 Sufficient SCDO:0000211 HP:0005305 Blood Clot in Cerebral Vein Cerebral Thrombosis Cerebral Vein Thrombosis Cerebral Venous Thrombosis HP:0005318 Inflammation of the blood vessels within the brain. http://purl.obolibrary.org/obo/HP_0005318 Sufficient SCDO:0000210 HP:0005318 Cerebral Vasculitis HP:0005518 Larger than normal size of erythrocytes. Macrocytosis refers to a mean cell volume (MCV) greater than 100 fL. If macrocytosis is an isolated abnormality, the amount of hemoglobin in the cell increases proportionately, so the mean cell hemoglobin concentration (MCHC) remains within normal limits. Sufficient SCDO:1000626 HP:0005518 Erythrocyte Macrocytosis High MCV Increased MCV Increased Mean Corpuscular Volume HP:0005560 Normal hemoglobin synthesis is characterized by production of equal amounts of alpha and beta globins. This term refers to a deviation from this pattern and is the main characteristic of the various forms of thalassemia. http://purl.obolibrary.org/obo/HP_0005560 Sufficient SCDO:0001383 HP:0005560 Imbalanced Hemoglobin Synthesis HP:0006689 A bacterial infection of the endocardium, the inner layer of the heart, which usually involves the heart valves. Check and show which source was used for the description and whether the description was adapted from the source. -- Provide source for additional info. Sufficient SCDO:0000099 HP:0006689 Infective Endocarditis Bacterial Endocarditis HP:0007018 Attention deficit hyperactivity disorder (ADHD) manifests at age 2-3 years or by first grade at the latest. The main symptoms are distractibility, impulsivity, hyperactivity, and often trouble organizing tasks and projects, difficulty going to sleep, and social problems from being aggressive, loud, or impatient. http://purl.obolibrary.org/obo/HP_0007018 Sufficient SCDO:0000090 HP:0007018 ADHD Attention Deficit Attention Deficit Disorder Attention Deficit-Hyperactivity Disorder Attention Deficits Childhood Attention Deficit/Hyperactivity Disorder Attention Deficit Hyperactivity Disorder HP:0007340 Weakness of the muscles of the legs. Sufficient SCDO:0000686 HP:0007340 Hind Limb Weakness Hindlimb Weakness Leg Weakness Lower Extremity Weakness Lower Limb Muscle Weakness Lower Limb Weakness Muscle Weakness in Lower Limbs Inability to perform rapid, alternating movements. Leg Weakness HP:0007902 Bleeding within the vitreous compartment of the eye. Sufficient SCDO:0001238 HP:0007902 Hemorrage Within the Vitreous Humor Vitreous Haemorrhage Vitreous Hemorrhage HP:0008245 A type of hypothyroidism that results from a defect in thyroid-stimulating hormone secretion. Provide source for additional info. http://purl.obolibrary.org/obo/HP_0008245 Sufficient SCDO:0001028 HP:0008245 TSH Deficient Hypothyroidism Thyroid Stimulating Hormone Deficiency Thyrotropin Deficiency Secondary Hypothyroidism HP:0008404 Onychodystrophy (nail dystrophy) refers to nail changes apart from changes of the color (nail dyschromia) and involves partial or complete disruption of the various keratinous layers of the nail plate. Sufficient SCDO:0000788 HP:0008404 Dystrophic Nails Onychodystrophy Poor nail formation Nail Dystrophy HP:0008682 Acute death of renal tubular cells that usually results from prolonged renal ischemia, nephrotoxins, or sepsis. Provide source for additional info. Can occur at any age. The clinical course of acute tubular necrosis may be divided into initiation, maintenance, and recovery phases. Renal ischemia (which can occur due to prolonged prerenal states), nephrotoxins, or sepsis. In sickle cell disease, may occur due to renal ischemia related to sickle crisis. Loss of kidney function, reduced urine output, elevated serum creatinine. Sufficient SCDO:0000020 HP:0008682 ATN Renal Tubular Necrosis Acute Tubular Necrosis HP:0009045 Rhabdomyolysis induced by exercise. http://purl.obolibrary.org/obo/HP_0009045 Sufficient SCDO:0001308 HP:0009045 Rhabdomyolysis with Exercise Exercise-Induced Rhabdomyolysis HP:0009830 Peripheral neuropathy is a general term for any disorder of the peripheral nervous system. http://purl.obolibrary.org/obo/HP_0009830 Symptoms depend on which nerve is damaged, and whether the damage affects one nerve, several nerves, or the whole body. Pain and numbness: Tingling or burning in the arms and legs may be an early sign of nerve damage. These feelings often start in your toes and feet. You may have deep pain. This often happens in the feet and legs. You may lose feeling in your legs and arms. Because of this, you may not notice when you step on something sharp. You may not notice when you touch something that is too hot or cold, like the water in a bathtub. You may not know when you have a small blister or sore on your feet. Numbness may make it harder to tell where your feet are moving and can cause a loss of balance. Muscle problems: Damage to the nerves can make it harder to control muscles. It can also cause weakness. You may notice problems moving a part of your body. You may fall because your legs buckle. You may trip over your toes. Doing tasks such as buttoning a shirt may be harder. You may also notice that your muscles twitch or cramp. Your muscles may become smaller. Problems with body organs: People with nerve damage may have problems digesting food. You may feel full or bloated and have heartburn after eating only a little food. Sometimes you may vomit food that has not been digested well. You may have either loose stools or hard stools. Some people have problems swallowing. Damage to the nerves to your heart may cause you to feel light-headed, or faint, when you stand up. Angina is the warning chest pain for heart disease and heart attack. Nerve damage may "hide" this warning sign. You should learn other warning signs of a heart attack. They are sudden fatigue, sweating, shortness of breath, nausea, and vomiting. Sufficient SCDO:0000884 HP:0009830 Peripheral Nerve Damage Peripheral Neuritis Peripheral Neuropathy HP:0010628 Facial nerve palsy is a dysfunction of cranial nerve VII (the facial nerve) that results in inability to control facial muscles on the affected side with weakness of the muscles of facial expression and eye closure. This can either be present in unilateral or bilateral form. - Provide source for additional info. Sufficient SCDO:0001315 HP:0010628 Bell's Palsy Cranial Nerve VII Palsy Facial Muscle Weakness of Muscles Innervated by CN VII Facial Nerve Paralysis Facial Palsy Facial Paralysis Seventh Cranial Nerve Palsy VIIth Cranial Nerve Palsy Facial Nerve Palsy HP:0010876 An abnormal level of a circulating protein in the blood. Sufficient SCDO:1000438 HP:0010876 Abnormality of Circulating Protein Level Blood Protein Disease Serum Protein Abnormality Abnormal Circulating Protein Level HP:0010885 A disease where there is cellular death (necrosis) of bone components due to interruption of the blood supply. No one is sure what causes the disease. Risk factors include: -- -- Long-term steroid treatment -- Alcohol abuse -- Joint injuries -- Having certain diseases, including arthritis and cancer -- Doctors use imaging tests and other tests to diagnose osteonecrosis. -- -- Treatments include medicines, using crutches, limiting activities that put weight on the affected joints, electrical stimulation and surgery. Sufficient SCDO:0000841 http://purl.bioontology.org/ontology/MEDLINEPLUS/C0029445 HP:0010885 AVN Aseptic Bone Necrosis Aseptic necrosis Avascular Bone Necrosis Avascular Necrosis Avascular Necrosis (AVN) Bone Infarction Bone Infarcts Bone Necrosis Ischemic Bone Necrosis Osteochondronecrosis The interruption of the blood supply may have many different causes such as rapid growth, heredity causes, trauma or overuse, anatomic conformation, dietary imbalances or secondary effects of other diseases. Osteonecrosis HP:0011001 An abnormal increase of bone mineral density, that is, of the amount of matter per cubic centimeter of bones which is often refered to as osteosclerosis. Osteosclerosis can be detected on radiological examination as an increased whiteness (density) of affected bones. Provide source for additional info. http://purl.obolibrary.org/obo/HP_0011001 Ischemia, chronic infection, and tumor formation, osteoarthritis, osteoma, hepatitis C, . May be caused by faulty bone resorption as a result of some abnormality involving osteoclasts. An increased whiteness (density) of affected bones. Sufficient SCDO:0000629 HP:0011001 Bone Sclerosis Increased Bone Density Osteosclerosis Osteosclerosis of Bones Increased Bone Mineral Density HP:0011007 The age group in which disease manifestations appear. http://purl.obolibrary.org/obo/HP_0011007 Sufficient SCDO:0003913 HP:0011007 Age of Onset HP:0011014 Abnormality of glucose homeostasis. Sufficient SCDO:1000283 HP:0011014 Abnormal Glucose Homeostasis HP:0011025 Abnormal functionality of the cardiovascular system. Sufficient SCDO:1000368 HP:0011025 Abnormal Cardiovascular System Physiology HP:0011106 A decrease in the amount of intravascular fluid, particularly in the volume of the circulating blood. Sufficient SCDO:0003035 HP:0011106 Depleted Blood Volume Hypovolemia HP:0011121 Any morphological abnormality of the skin. Sufficient SCDO:1000374 HP:0011121 Abnormality of Skin Morphology HP:0011122 Any abnormality of the physiological function of the skin. Sufficient SCDO:1000375 HP:0011122 Abnormality of Skin Physiology HP:0011123 The presence of inflammation of the skin. That is, an abnormality of the skin resulting from the local accumulation of fluid, plasma proteins, and leukocytes. Sufficient SCDO:0001071 HP:0011123 Abnormal Tendency to Infections of the Skin Dermatitis Inflammatory Abnormality of the Skin Inflammatory Skin Disease Maculopapular Rash Skin Inflammation HP:0011410 Delivery of a fetus through surgical incisions made through the abdominal wall (laparotomy) and the uterine wall (hysterotomy). http://purl.obolibrary.org/obo/HP_0011410 Sufficient SCDO:0000168 HP:0011410 Caesarian Section HP:0011413 Shoulder dystocia occurs when the fetal anterior shoulder impacts against the maternal symphysis following delivery of the vertex. Sufficient SCDO:0001045 HP:0011413 Shoulder Dystocia HP:0011675 Any cardiac rhythm other than the normal sinus rhythm. Such a rhythm may be either of sinus or ectopic origin and either regular or irregular. An arrhythmia may be due to a disturbance in impulse formation or conduction or both. http://purl.obolibrary.org/obo/HP_0011675 Sufficient SCDO:0009619 HP:0011675 Abnormal Heart Rate Abnormality of Cardiac Conduction Arrhythmias Cardiac Arrhythmia Cardiac Arrhythmias Cardiac Conduction Abnormalities Cardiac Conduction Defects Cardiac Rhythm Disturbances Heart Rhythm Disorders Irregular Heart Beat Irregular Heartbeat Arrhythmia HP:0011695 Hemorrhage into the parenchyma of the cerebellum. Need to include this term mentioned here to the SCDO: -- obstructive hydrocephalus Sufficient SCDO:0000201 HP:0011695 Cerebellar Hemorrhage HP:0011856 An appetite for and the persistent ingestion of non-food substances such as clay. In order to diagnose pica, this behavior must have persisted over a period of at least one month. http://purl.obolibrary.org/obo/HP_0011856 Sufficient SCDO:0000904 HP:0011856 Pica HP:0011868 Pain in the lower back and hip radiating in the distribution of the sciatic nerve. Provide source for additional info. Terms to add to therapeutics for linking via "is treated with" obj property: Local heat, acupuncture, physical therapy, surgery http://purl.obolibrary.org/obo/HP_0011868 Compression of a spinal nerve root by disc or arthritic spur, degenerative changes involvind main structures, disc protrusion, congenital abnormalities of the bony spinal column, infection, inflammation, neoplasm, vascular diseases. Sufficient SCDO:0001024 HP:0011868 Sciatica HP:0011873 Abnormal number of platelets per volume of blood. In a healthy adult, a normal platelet count is between 150,000 and 450,000 per microliter of blood. Sufficient SCDO:1000617 HP:0011873 Abnormal Platelet Count HP:0011886 Bleeding in the anterior chamber of the eye. http://purl.obolibrary.org/obo/HP_0011886 Sufficient SCDO:0000597 HP:0011886 Hyphema HP:0011893 Number of leukocytes per volume of blood beyond normal limits. Sufficient SCDO:1000613 HP:0011893 Abnormal White Blood Cell Count Abnormal Leukocyte Count HP:0011897 Increased number of neutrophils circulating in blood. Sufficient SCDO:1000447 HP:0011897 Neutrophilia HP:0011904 Hemoglobin F (HbF) contains two globin alpha chains and two globin gamma chains. It is the main form of hemoglobin in the fetus during the last seven months of intrauterine development and in the half year of postnatal life. In adults it normally makes up less than one percent of all hemoglobiin. This term refers to an increase in HbF above this limit. In beta thalassemia major, it may represent over 90 percent of all hemoglobin, and in beta thalassemia minor it may make up between 0.5 to 4 percent. http://purl.obolibrary.org/obo/HP_0011904 Sufficient SCDO:0000888 HP:0011904 Increased Haemoglobin F Persistence of Hemoglobin F Raised Hemoglobin F Increased Hemoglobin F HP:0011906 A reduction in the ratio of production of beta globin to that of alpha globin. This is the major abnormality in the various forms of beta thalassemia. http://purl.obolibrary.org/obo/HP_0011906 Sufficient SCDO:0001709 HP:0011906 Increased Alpha/Beta Synthesis Ratio Reduced Beta/Alpha Synthesis Ratio HP:0011907 A reduction in the ratio of production of alpha globin to that of beta globin. This is the major abnormality in the various forms of alpha thalassemia. http://purl.obolibrary.org/obo/HP_0011907 Sufficient SCDO:0006404 HP:0011907 Increased Beta/Alpha Synthesis Ratio Reduced Alpha/Beta Synthesis Ratio HP:0011950 Inflammation of the bronchioles. http://purl.obolibrary.org/obo/HP_0011950 Sufficient SCDO:0005490 HP:0011950 Bronchiolitis HP:0011991 A deviation from the normal range of neutrophil cell counts in the circulation. Sufficient SCDO:1000446 HP:0011991 Abnormal Neutrophil Cell Number Abnormal Neutrophil Count HP:0012100 An abnormal concentration of creatinine in the blood. Sufficient SCDO:1000541 HP:0012100 Abnormal Blood Creatinine Level Abnormal Serum Creatinine Level Creatinine Levels Abnormal Abnormal Circulating Creatinine Level HP:0012101 An abnormally reduced amount of creatinine in the blood. Sufficient SCDO:1000648 HP:0012101 Low Blood Creatinine Low Serum Creatinine Reduced Creatinine Levels Decreased Serum Creatinine HP:0012203 A fungal infection of the toenails or fingernails that tends to cause the nails to thicken, discolor, disfigure, and split. Sufficient SCDO:0000831 Medscape: Onychomycosis: Author: Antonella Tosti, MD; Chief Editor: Dirk M Elston, MD et al.. HP:0012203 has disease stage: Distal lateral subungual onychomycosis (DLSO), White superficial onychomycosis (WSO), Proximal subungual onychomycosis (PSO), Endonyx onychomycosis (EO), Candidal onychomycosis. Is characterised by: Disfigured nails, pain, paraesthesia, loss of dexterity, difficulty walking, standing, exercise. Onychomycosis HP:0012229 An increased white blood cell count in the cerebrospinal fluid. http://purl.obolibrary.org/obo/HP_0012229 Sufficient SCDO:0000212 HP:0012229 CSF Pleocytosis Increased Leukocyte Count in CSF Cerebrospinal Fluid Pleocytosis HP:0012243 A structural or developmental anomaly of any of the tissues involved in the genital system. Sufficient SCDO:0009817 HP:0012243 Abnormal Genital System Morphology Abnormal Reproductive System Morphology HP:0012282 An exanthema consisting of widespread pink-to-red macules (flat spots of 2-10 mm in diameter) or papules (red bumps) that blanch with pressure. The macules and papules may cluster and merge to form sheets over several days. Sufficient SCDO:0000770 HP:0012282 A morbilliform rash is said to resemble the rash of measles, rubella or scarlet fever, thus mimicking viral and bacterial exanthemas. Morbilliform Rash HP:0012330 An inflammation of the kidney involving the parenchyma of kidney, the renal pelvis and the kidney calices. http://purl.obolibrary.org/obo/HP_0012330 Sufficient SCDO:0005758 HP:0012330 Pyelonephritis HP:0012379 An altered ability of any enzyme or their cofactors to act as catalysts. This term includes changes due to altered levels of an enzyme. Sufficient SCDO:1000665 HP:0012379 Abnormal Enzyme/Coenzyme Activity HP:0012418 An abnormally low level of blood oxygen. http://purl.obolibrary.org/obo/HP_0012418 Sufficient SCDO:0000604 HP:0012418 Decreased Partial Pressure of Oxygen Low Blood Oxygen Level Hypoxemia HP:0012444 Partial or complete wasting (loss) of brain tissue that was once present. Sufficient SCDO:0000089 HP:0012444 Brain Atrophy Brain Degeneration Brain Wasting Atrophic Brain HP:0012465 An increased level of iron in liver tissues. http://purl.obolibrary.org/obo/HP_0012465 Sufficient SCDO:0000425 HP:0012465 Increased Iron Concentration in Liver Increased Liver Iron Level This abnormality can be measured by liver biopsy or by hepatic magnetic resonance imaging. Equivalents Elevated Hepatic Iron Concentration HP:0012532 Persistent pain, usually defined as pain that has lasted longer than 3 to 6 months. Sufficient SCDO:0001415 HP:0012532 Long-Lasting Pain Chronic Pain HP:0012574 Increased numbers of mesangial cells per glomerulus, defined as four or more nuclei in a peripheral mesangial segment. Sufficient SCDO:0006481 HP:0012574 Mesangial Proliferation Mesangial Hypercellularity HP:0012587 Hematuria that is visible upon inspection of the urine. http://purl.obolibrary.org/obo/HP_0012587 Sufficient SCDO:0008145 HP:0012587 Bloody Urine Gross Hematuria Macroscopic Hematuria HP:0012594 The presence of mildly increased concentrations of albumin in the urine (in adults, 30-150 mg per day). http://patient.info/doctor/microalbuminuria Sufficient SCDO:0000764 Chronic kidney disease: early identification and management of chronic kidney disease in adults in primary and secondary care; NICE Clinical Guidelines (July 2014) HP:0012594 Micro-albuminuria Microalbuminuria Mildly Increased Albuminuria Moderately Increased Albuminuria The criteria for clinically significant proteinuria have been changed from an albumin-creatinine ratio (ACR) of 30 mg/mmol or more to 3 mg/mmol or more. This is because there is evidence that the risk of adverse outcomes is a continuum and starts at an ACR well below 30 mg/mmol. Low Level Albuminuria HP:0012638 A functional anomaly of the nervous system. Sufficient SCDO:1000765 HP:0012638 Abnormality of Nervous System Physiology Abnormal Nervous System Physiology HP:0012639 A structural anomaly of the nervous system. Sufficient SCDO:1000764 HP:0012639 Abnormal Shape of Nervous System Abnormality of Nervous System Morphology Abnormal Nervous System Morphology HP:0012735 A sudden, audible expulsion of air from the lungs through a partially closed glottis, preceded by inhalation. Sufficient SCDO:0004069 HP:0012735 Cough HP:0012759 A deviation from normal of the neurological development of a child, which may include any or all of the aspects of the development of personal, social, gross or fine motor, and cognitive abilities. This term should be used to describe abnormalities with onset in the developmental period. http://purl.obolibrary.org/obo/HP_0012759 Sufficient SCDO:0000800 HP:0012759 Neurodevelopmental Abnormality HP:0012819 Inflammation of the myocardium. Sufficient SCDO:0004203 HP:0012819 Myocarditis can be caused by a variety of bacterial and viral infections. Enteroviruses, especially coxsackievirus B, are often associated with acute myocarditis. However, with the advent of genetic analysis, adenovirus and parvovirus B19 have also been found to be frequent causes of myocarditis. Exposure to drug treatment, physical stimuli such as radiation and heat, metabolic disorders, immune disorders, and pregnancy are also causes of myocarditis. Many cases of myocarditis are idiopathic. Myocarditis presents with non-specific symptoms including chest pain, dyspnoea, and palpitations, and thus often mimics more common disorders such as coronary artery disease. In some patients, cardiac MRI and endomyocardial biopsy can help identify myocarditis, predict risk of cardiovascular events, and guide treatment. Myocarditis HP:0020054 Any functional abnormality of erythrocytes (red-blood cells). Sufficient SCDO:1000286 HP:0020054 Abnormal Erythrocyte Physiology HP:0020058 Any deviation from the normal number of red blood cells per volume in the circulation. Sufficient SCDO:1000608 HP:0020058 Abnormal RBC Count Abnormal Red Blood Cell Count HP:0020059 An abnormal elevation above the normal number of red blood cells per volume in the circulation. Sufficient SCDO:1000610 HP:0020059 Increased RBC Count Increased Red Blood Cell Count HP:0020060 An abnormal reduction below the normal number of red blood cells per volume in the circulation. Sufficient SCDO:1000609 HP:0020060 Decreased RBC Count Decreased Red Blood Cell Count HP:0020061 Any deviation from the normal concentration of hemoglobin in the blood. It might seem wrong to place this class here, but note that a change in hemoglobin concentration affects the size/volume and hence morphology of erythrocytes. Perhaps add sub-classes "Increased hemoglobin concentration" and "Decreased hemoglobin concentration" from HPO...their descriptions don't seem quite right though (should it not rather be "in the erythrocytes", not "in the circulation"? Sufficient SCDO:1000186 SCDO (Jade Hotchkiss) HP:0020061 Abnormal Hemoglobin Concentration HP:0020062 An abnormal reduction below normal hemoglobin concentration in the circulation. Sufficient SCDO:1000377 HP:0020062 Decreased Hemoglobin Concentration HP:0020063 An abnormal elevation above normal hemoglobin concentration in the circulation. Sufficient SCDO:1000378 HP:0020063 Increased Hemoglobin Concentration HP:0025031 Any anomaly of the digestive system, a collection of organs that is made up of the gastrointestinal tract and the liver, pancreas, and gallbladder. The gastrointestinal tract is a series of hollow organs joined in a long, twisting tube from the mouth to the anus, including the mouth, esophagus, stomach, small intestine, large intestine and anus. Kaeda JS, Roper D, Srivastava P, et al. Severe hemolytic anemia associated with the homozygous state for an unstable hemoglobin variant (Hb Bushwick). Blood 1995; 86:1977. http://purl.obolibrary.org/obo/HP_0025031 Sufficient SCDO:0000335 HP:0025031 Abnormality of the Digestive System HP:0025065 A deviation from normal of the mean corpuscular volume, or mean cell volume (MCV) of red blood cells, usually taken to be 80 to 100 femtoliters. Sufficient SCDO:1000624 HP:0025065 Abnormal Erythrocyte Volume Abnormal MCV Abnormal Mean Corpuscular Volume HP:0025066 A reduction from normal of the mean corpuscular volume, or mean cell volume (MCV) of red blood cells (usually defined as an MCV below 80 femtoliters). Sufficient SCDO:1000625 HP:0025066 Decreased MCV Low MCV Microcytosis Reduced Erythrocyte Volume Decreased Mean Corpuscular Volume HP:0025142 A symptom or manifestation indicating a systemic or general effect of a disease and that may affect the general well-being or status of an individual. Sufficient SCDO:1000269 HP:0025142 Systemic Symptom Constitutional Symptom HP:0025435 An elevated level of the enzyme lactate dehydrogenase in serum. Sufficient SCDO:1000652 HP:0025435 High Lactate Dehydrogenase Level Increased Lactate Dehydrogenase Level HP:0025546 Deviation from the normal Hgb/Hct; the average hemoglobin concentration in a given volume of packed red cells, calculated from the hemoglobin therein and the hematocrit, in erythrocyte indices. Sufficient SCDO:1000631 HP:0025546 Abnormal MCHC Abnormal Mean Cell Haemoglobin Concentration Abnormal Mean Cell Hb Concentration Abnormal Mean Cell Hemoglobin Concentration Abnormal Mean Corpuscular Haemoglobin Concentration Abnormal Mean Corpuscular Hb Concentration Abnormal Mean Corpuscular Hemoglobin Concentration HP:0025547 Less than the normal Hgb/Hct; the average hemoglobin concentration in a given volume of packed red cells, calculated from the hemoglobin therein and the hematocrit, in erythrocyte indices. Sufficient SCDO:1000635 HP:0025547 Decreased MCHC Decreased Mean Corpuscular Haemoglobin Concentration Low MCHC Low Mean Corpuscular Haemoglobin Concentration Low Mean Corpuscular Hemoglobin Concentration Reduced Mean Corpuscular Haemoglobin Concentration Reduced Mean Corpuscular Hemoglobin Concentration Decreased Mean Corpuscular Hemoglobin Concentration HP:0025548 Greater than the normal Hgb/Hct; the average hemoglobin concentration in a given volume of packed red cells, calculated from the hemoglobin therein and the hematocrit, in erythrocyte indices. Sufficient SCDO:1000636 HP:0025548 High MCHC High Mean Corpuscular Haemoglobin Concentration High Mean Corpuscular Hemoglobin Concentration Increased MCHC Increased Mean Corpuscular Haemoglobin Concentration Increased Mean Corpuscular Hemoglobin Concentration HP:0025636 Inflammation of the inner lining of the uterus Local accumulation of fluid, plasma proteins, and leukocytes in the endometrium. Provide source for additional info. http://purl.obolibrary.org/obo/MP_0009360 Sufficient SCDO:0000433 HP:0025636 Endometrial Inflammation Endometrium Inflammation Endometritis HP:0030049 A collection of pus, immune cells, and other material in the brain. http://purl.obolibrary.org/obo/HP_0030049 Sufficient SCDO:0000159 HP:0030049 Brain abscess usually results from a bacterial or fungal infection. Brain Abscess HP:0030050 An abnormal phenomenon characterized by a classic tetrad of excessive daytime sleepiness with irresistible sleep attacks, cataplexy (sudden bilateral loss of muscle tone), hypnagogic hallucination, and sleep paralysis. Sufficient SCDO:0000790 HP:0030050 Narcolepsy HP:0030058 An irreversible distortion of the morphology of an erythrocyte such that the cells are elongated and curved, resembling the blade of a sickle (the hand-held agricultural tool traditionally used to harvest grains). Sufficient SCDO:1000246 HP:0030058 Banana Cell Drepanocyte Sickle Cell Sickled Erythrocyte Sickled Red Blood Cell Sickled Erythrocyte HP:0030127 The growth of endometrial tissue outside the uterus. Provide source for additional info. http://purl.obolibrary.org/obo/HP_0030127 Sufficient SCDO:0000432 HP:0030127 Endometriosis HP:0030243 An obstruction in the veins of the liver caused by a blood clot (thrombosis). http://purl.obolibrary.org/obo/HP_0030243 Sufficient SCDO:0001673 HP:0030243 Blood Clot in Liver Vein Hepatic Vein Thrombosis Blood Clot in Liver Vein HP:0030248 A clot that obstructs blood flow in a mesenteric vein (the superior and the inferior mesenteric vein drain blood from the small and large intestine). Sufficient SCDO:0004437 HP:0030248 Blood Clot in Mesenteric Vein Mesenteric Venous Thrombosis HP:0030680 Any structural anomaly of the heart and great vessels. Sufficient SCDO:1000369 HP:0030680 Abnormal Cardiovascular System Morphology HP:0031368 A hole (perforation) in the wall of the intestine. Sufficient SCDO:1000434 HP:0031368 Intestinal Perforation HP:0031456 A pregnancy in which the fertilized egg inserts in a location outside of the main cavity of the uterus (usually in the Fallopian tube). Sufficient SCDO:0000413 HP:0031456 Ectopic Pregnancy HP:0031956 An abnormally high concentration in the circulation of aspartate aminotransferase (AST). Sufficient SCDO:1000661 HP:0031956 Aspartate Aminotransferase Increased Elevated Serum AST Elevated Serum Glutamic Oxaloacetic Transaminase Increased Aspartate Aminotransferase Elevated Serum Aspartate Aminotransferase HP:0031964 An abnormally high concentration in the circulation of alanine aminotransferase (ALT), which is an enzyme that catalyzes the transfer of amino groups to form the hepatic metabolite oxaloacetate. ALT is found abundantly in the cytosol of the hepatocyte. ALT activity in the liver is about 3000 times that of serum activity. Thus, in the case of hepatocellular injury or death, release of ALT from damaged liver cells increases measured ALT activity in the serum. Although it is generally thought to be specific to the liver, it is also found in the kidney, and, in much smaller quantities, in heart and skeletal muscle cells. Sufficient SCDO:1000659 HP:0031964 Alanine Aminotransferase Increased Elevated Serum Glutamic-Pyruvic Transaminase Elevated serum ALT Elevated Serum Alanine Aminotransferase HP:0032180 An abnormal level of an analyte measured in the blood. Sufficient SCDO:1000437 HP:0032180 Abnormal Circulating Metabolite Concentration HP:0032224 The ABO histo-blood group consists of two antigens (A and B antigens) and four blood types (types A, B, AB, and O). The A and B antigens are the product of the ABO gene and are autosomal codominant. The group O phenotype is an autosomal-recessive phenotype due to the homozygous inheritance of two null ABO alleles. Group O individuals express the H antigen, the biosynthetic precursor to A and B antigens. ABO, therefore, is the blood type, whereas A, B, and H refer to the antigens. The ABO system consists of A and B antigens and antibodies against these antigens. Sufficient SCDO:1000581 HP:0032224 ABO Blood Group HP:0045040 A deviation from the normal serum concentration/activity of lactate dehydrogenase (LDH), which catalyzes the reduction of pyruvate to form lactate. Sufficient SCDO:1000683 HP:0045040 Abnormal Lactate Dehydrogenase Level HP:0045048 An elevated concentration in the blood of hemoglobin A2 (HbA2), which is a normal variant of hemoglobin A that consists of two alpha and two delta chains and is normally present at low levels in adults but may be increased in beta thalassemia. http://purl.obolibrary.org/obo/HP_0045048 Sufficient SCDO:0000630 HP:0045048 Increased HbA2 Hemoglobin Increased Hemoglobin A2 HP:0100601 An acute and life-threatening complication of pregnancy, which is characterized by the appearance of tonic-clonic seizures, usually in a patient who had developed pre-eclampsia. Eclampsia includes seizures and coma that happen during pregnancy but are not due to preexisting or organic brain disorders. Sufficient SCDO:0000411 HP:0100601 Eclampsia HP:0100602 Pregnancy-induced hypertension in association with significant amounts of protein in the urine. http://purl.obolibrary.org/obo/HP_0100602 Sufficient SCDO:0000918 HP:0100602 Pre-Eclampsia Preeclampsia HP:0100614 A general term for inflammation of the muscles without respect to the underlying cause. Provide source for additional info. http://purl.obolibrary.org/obo/HP_0100614 Sufficient SCDO:0000785 HP:0100614 Muscle Inflammation Myositis HP:0100749 An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) localized to the chest. Sufficient SCDO:0001988 HP:0100749 Thoracic Pain Chest Pain HP:0100774 Excessive growth or abnormal thickening of bone tissue. http://purl.obolibrary.org/obo/HP_0100774 Sufficient SCDO:0000591 HP:0100774 Bone Hypertrophy Bone Overgrowth Hyperostosis HP:0100806 Severe systemic inflammatory response to infection. Perhaps remove here and only keep below "Abnormality of the Immune System"? Source needed for additional information. Perhaps include different types of sepsis (see under D018805 in MESH)? http://purl.obolibrary.org/obo/HP_0100806 Sufficient SCDO:0001039 HP:0100806 caused by: Bacteria and fungus mainly characterised by: Systematic manifestations of inflammation has disease stage: Mild, moderate, severe Sepsis HP:0100820 Inflammatory or noninflammatory diseases affecting the glomeruli of the nephron. http://purl.obolibrary.org/obo/HP_0100820 Sufficient SCDO:0000459 HP:0100820 Diseased Glomeruli Glomerulopathies Glomerulopathy HP:0200042 A discontinuity of the skin exhibiting loss of the epidermis and often portions of the dermis and subcutaneous fat. Find source for additional info http://purl.obolibrary.org/obo/HP_0200042 Sufficient SCDO:0001074 HP:0200042 Open Skin Sore Skin Ulcers Skin Ulcer HP:0500015 Abnormal test result of cardiovascular physiology. Sufficient SCDO:1000266 HP:0500015 Abnormal Cardiac Test HsapDv:0000000 A spatiotemporal region encompassing some part of the life cycle of an organism. See specific stages in the "Human Developmental Stages Ontology" http://purl.obolibrary.org/obo/HsapDv_0000000 Sufficient SCDO:0007384 HsapDv:0000000 Developmental Stage Human Life Cycle Stage ICO:0000036 A date specification that designates when an informed consent form was signed. Sufficient SCDO:1000531 ICO:0000036 Date Subject Signed Consent Informed Consent Form Signing Date Date of Signing Consent ICO:0000157 An informed consent by the parent/guardian of a child or a minor to consent to give permission for the child/minor to be included in research. Sufficient SCDO:0009293 ICO:0000157 Parental Informed Consent Process Parental Permission Parental Permission Consent Parental Consent ICO:0000179 An informed consent for an unspecified range of future research subject to a few content and/or process restrictions. Sufficient SCDO:0008115 ICO:0000179 Broad Consent ICO:0000228 A planned process in which data possessed by one person or organization is shared with one or more other persons or organizations. Sufficient SCDO:0009586 ICO:0000228 Act of Data Sharing Data Sharing ICO:0000255 A directive information entity that prescribes some process for withdraw from another planned process. Sufficient SCDO:1000428 ICO:0000255 Withdrawal from Participation Directive Participant Withdrawal Process ICO:0000278 A descriptive information content entity that describes how biospecimens will be used. Sufficient SCDO:1000456 ICO:0000278 Description of Future Biospecimen Use ICO:0000293 A directive information entity that prescribes the information that is permitted to be shared or the processes for sharing that information. Sufficient SCDO:1000407 ICO:0000293 Data Sharing Directive Data Sharing Agreement ICO:0000304 A descriptive information content entity that describes how data will be used. Sufficient SCDO:1000453 ICO:0000304 Description of Future Data Use ICO:0000305 A descriptive information content entity that describes future use of material or information. Sufficient SCDO:1000454 ICO:0000305 Description of Future Use IDOMAL:0000122 The use of antimalarial drugs for the prevention of infection. Sufficient SCDO:1000668 IDOMAL:0000122 Malaria Chemoprophylaxis IDOMAL:0000592 Any process carried out to determine the condition of a patient's spleen. Needs relating to Splenomegaly phenotype. http://purl.obolibrary.org/obo/IDOMAL_0000592 Sufficient SCDO:0001101 IDOMAL:0000592 Spleen Examination IDOMAL:50000026 A permanent change in the DNA sequence of a gene that alters the genetic message carried by that gene. Perhaps include here an "Alpha Thalassemia Mutation" sub-class? Could use the current description for "Alpha-Globin Locus Deletion" and instead give "Alpha-Globin Locus Deletion" a description similar to that of "Beta-Globin Locus Deletion" http://purl.obolibrary.org/obo/IDOMAL_50000026 Sufficient SCDO:0001370 IDOMAL:50000026 Mutation IDO:0000515 An organism population whose members are particpating in non-parasitic symbiosis with a particular host. http://purl.obolibrary.org/obo/IDO_0000515 Sufficient SCDO:0000755 IDO:0000515 Normal Resident Microbiota Population Normal Resident Microflora Population Microbiome IDO:0000560 A material entity bearing an antifungal disposition. http://purl.obolibrary.org/obo/IDO_0000560 Sufficient SCDO:1000019 IDO:0000560 Antifungal IDO:0000586 A part of an extended organism that itself has as part a population of one or more infectious agents and that (1) exists as a result of processes initiated by members of the infectious agent population and is (2) clinically abnormal in virtue of the presence of this infectious agent population, or (3) has a disposition to bring clinical abnormality to immunocompetent organisms of the same Species as the host (the organism corresponding to the extended organism) through transmission of a member or offspring of a member of the infectious agent population. Perhaps use Bacterial Infection and Viral Infection as modifiers? Include here "transfusion-related hepatitis infections" and or "viral hepatitis" (See paper "Liver involvement in sickle cell disease" by Emel GÜRKAN et al.) Sufficient SCDO:0000635 IDO:0000586 Infection MP:0001212 Focal pathological and/or inflammatory changes characterized by alteration in the size, shape and organization of the cellular components of the skin. Sufficient SCDO:0001072 MP:0001212 Skin Lesions MP:0001589 Anomalies in the average levels of hemoglobin contained in an erythrocyte. Sufficient SCDO:1000632 MP:0001589 Abnormal MCH Abnormal Mean Cell Hemoglobin Abnormal Mean Cell Hemoglobin Level Abnormal Mean Corpuscular Hemoglobin Level Abnormal Mean Corpuscular Hemoglobin MP:0001762 Increased volume of urine produced and excreted. Provide source for additional info. http://purl.obolibrary.org/obo/MP_0001762 Sufficient SCDO:0000395 MP:0001762 Increased Urine Output Increased Urine Volume Polyuria Clinicians sometimes mistakenly label increased urinary frequency as polyuria (increased urine output); Though rarely used, pollakisuria (or pollakiuria) is the correct term for increased frequency of urination. Diuresis MP:0001792 Reduced ability or inability to self-repair and close wounds. Sufficient SCDO:0000622 MP:0001792 Delayed Wound Healing Impaired Wound Repair Impaired Wound Healing MP:0002081 Death anytime within the perinatal period. Sufficient SCDO:0000883 MP:0002081 Perinatal Lethality Perinatal Death MP:0002118 Anomaly in the processes involved in the maintenance of an internal equilibrium of lipids in the fluids and tissues. Sufficient SCDO:1000284 MP:0002118 Abnormal Lipid Homeostasis MP:0002329 Anomaly in the amount of oxygen and carbon dioxide in the blood. Sufficient SCDO:1000810 MP:0002329 Abnormal Blood Gas Level MP:0002412 Greater likelihood that an organism will develop ill effects from a bacterial infection or from components of or toxins produced by bacteria. http://purl.obolibrary.org/obo/MP_0002412 Sufficient SCDO:0000632 MP:0002412 Decreased Resistance to Bacterial infection Characterised by: Repeated/recurrent local or systemic bacterial infections. Caused by: Multifactorial generally factors ultimately cause impaired immunity. Increased Susceptibility to Bacterial Infection MP:0003224 A retrogressive impairment of function or destruction of the functional cells of the nervous system that receive, conduct, and transmit impulses. Provide source for additional info. Usually in the elderly persons. Aging associated with most disorders Multifactorial causes such as program cell death, genetic mutations, protein misfolding and intracellular mechanisms Multiple disease entities such as alzhiemers disease, parkinsons disease , huntington's disease and amylotrophic lateral sclerosis Sufficient SCDO:0000802 http://www.neurodegenerationresearch.eu/about/what/ MP:0003224 Nerve Degeneration Nerve Degenerations Neuron Degenerations Neuron Degeneration MP:0005376 The observable morphological and physiological characteristics related to a state of equilibrium in the body with respect to various functions and to chemical composition of the fluids and tissues or the processes that cause many of the chemical changes in living mammalian organisms that are manifested through development and lifespan. Sufficient SCDO:1000811 MP:0005376 Homeostasis Phenotype Homeostasis/Metabolism Phenotype Metabolism/Homeostasis Phenotype MP:0005533 Greater than the level of heat natural to a living being. Sufficient SCDO:1000761 MP:0005533 Raised Body Temperature Increased Body Temperature MP:0005534 Less than the level of heat natural to a living being. Sufficient SCDO:1000762 MP:0005534 Reduced Body Temperature Decreased Body Temperature MP:0005535 Deviation in the level of heat natural to a living being. Sufficient SCDO:1000760 MP:0005535 Abnormal Body Temperature MP:0005561 Greater than the average levels of hemoglobin contained in an erythrocyte. Sufficient SCDO:1000634 MP:0005561 High MCH High Mean Corpuscular Hemoglobin Increased MCH Increased Mean Cell Hemoglobin Increased Mean Corpuscular Hemoglobin MP:0005562 Less than the average levels of hemoglobin contained in an erythrocyte. Sufficient SCDO:1000633 MP:0005562 Decreased MCH Decreased Mean Cell Hemoglobin Low MCH Low Mean Corpuscular Hemoglobin Decreased Mean Corpuscular Hemoglobin MP:0009568 A measure (DImax) related to cell surface area, of the changeability of the membrane of circulating oxygen transporting cells as a function of physiologically relevant osmolality at a constant applied shear stress. Sufficient SCDO:1000277 MP:0009568 Abnormal Red Blood Cell Deformability MP:0009642 Anomaly in the processes involved in the maintenance of an internal equilibrium of various functions or chemical or protein composition of the blood. Sufficient SCDO:1000809 MP:0009642 Abnormal Blood Chemistry Blood Chemistry Abnormalities Abnormal Blood Homeostasis MP:0010066 An anomaly in the coefficient of variance (reference range) of the red blood cell volume for an organism. Sufficient SCDO:1000639 MP:0010066 Abnormal Erythrocyte Distribution Width Abnormal RDW Abnormal Red Blood Cell Distribution Width MP:0010067 Higher than normal coefficient of variance (reference range) of the red blood cell volume for an organism. Sufficient SCDO:1000641 MP:0010067 High RCDW High RDW High Red Blood Cell Distribution Width Increased Erythrocyte Distribution Width Increased RCDW Increased RDW Increased Red Blood Cell Distribution Width MP:0010068 Lower than normal coefficient of variance (reference range) of the red blood cell volume for an organism. Sufficient SCDO:1000640 MP:0010068 Decreased Erythrocyte Distribution Width Decreased RCDW Decreased RDW Low RCDW Low RDW Low Red Blood Cell Distribution Width Reduced RCDW Reduced RDW Reduced Red Blood Cell Distribution Width Decreased Red Blood Cell Distribution Width MP:0010163 Destruction of erythrocytes such that hemoglobin is released from the cells; may occur by many different causal agents such as antibodies, bacteria, chemicals, temperature, and changes in tonicity. Sufficient SCDO:0009017 MP:0010163 Erythrocytolysis Erythrolysis Haematolysis Haemolysis Hematolysis Hemolyses Hemolysis MP:0011468 Any anomaly in the amount in the urine of a carboxylic acid containing one or more amino groups (-NH2) and a carboxyl (-COOH) group. Sufficient SCDO:1000653 MP:0011468 Abnormal Urine Amino Acid Level MP:0011469 Any change in the amount of creatinine in the urine Sufficient SCDO:1000654 MP:0011469 Abnormal Urine Creatinine Level MP:0011470 An increased amount of creatinine in the urine compared to the normal state. Sufficient SCDO:1000656 MP:0011470 Increased Urine Creatinine Level MP:0011471 a reduced amount of creatinine in the urine compared to the normal state Sufficient SCDO:1000655 MP:0011471 Low Urine Creatinine Level Reduced Urine Creatinine Level Decreased Urine Creatinine Level MP:0013305 Inability of the kidneys to produce either a concentrated or a dilute urine; refers to a state in chronic renal disease in which the kidney cannot form urine with a higher or a lower specific gravity (concentration) than that of protein-free plasma; the specific gravity of the urine becomes fixed, irrespective of the fluid intake. http://purl.obolibrary.org/obo/MP_0013305 Sufficient SCDO:0000667 MP:0013305 Impaired Urine-Concentrating Ability Urine Concentrating Defect Urine specific gravity is similar to that of plasma (1.008-1.012). Isosthenuria NBO:0000131 A drinking behavior associated with the intake of alcohol. http://purl.obolibrary.org/obo/NBO_0000131 Sufficient SCDO:0000039 NBO:0000131 Alcohol Consumption Alcohol Intake NCIT:65495 A drug used to treat depression and peripheral neuropathy (pain, numbness, tingling, burning, or weakness in the hands or feet) that can occur with diabetes. http://purl.obolibrary.org/obo/NCIT_C65495 Sufficient SCDO:0006467 NCIT:65495 Cymbalta Duloxetine HCl N-methyl-3-(1-naphthalenyloxy)-3-(2-thiophene)propanamide Duloxetine NCIT:C101217 An examination of the retina of the eye using an ophthalmoscope. http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C101217 Sufficient SCDO:0001009 NCIT:C101217 Fundoscopy Retinal Examination NCIT:C102531 A finding indicating the presence of an inflammatory or neoplastic cellular infiltrate in the lung parenchyma. Sufficient SCDO:0007383 NCIT:C102531 Lung Infiltrate Pulmonary Infiltrate NCIT:C102988 A project to develop standards for the collection and analysis of patient-reported health status data using a system of highly reliable, precise measures for physical, mental, and social well-being. Patients are asked a series of rigorously reviewed questions covering common domains and metrics across differing conditions and treatments. The questions can be administered in short forms or adaptively through computerized adaptive testing and reports can be generated to allow clinicians to better understand how treatments might affect the quality of life of their patients. Sufficient SCDO:0000871 Bevans, M., Ross, A., & Cella, D. (2014). Patient-Reported Outcomes Measurement Information System (PROMIS): Efficient, standardized tools to measure self-reported health and quality of life. Nursing Outlook, 62, 339-345. Dampier C, Barry V, Gross HE, Lui Y, Thornburg CD, DeWalt DA, Reeve BB. (2016). Initial Evaluation of the Pediatric PROMIS® Health Domains in Children and Adolescents With Sickle Cell Disease. Pediatric Blood & Cancer. Feb 19. doi: 10.1002/pbc.25944. DeWitt, E. M., Barnett, K., Farrell, J., Revicki, D., Carle, A., Cook, K., Sherry, D. D. (2014). A164: Development of pediatric item banks to measure pain behavior in the Patient-Reported Outcomes Measurement Information System. Arthritis & Rheumatology, 66(Suppl. 11), S212-S2121. NCIT:C102988 PROMIS Patient Reported Outcomes Measurement Information System Patient Reported Outcomes Measurement Information System (PROMIS) NCIT:C103165 The kind of visit undertaken by the subject within a study, such as inpatient, outpatient, telephone, etc. Sufficient SCDO:1000852 NCIT:C103165 Subject Visit Type NCIT:C103270 The release from the requirement to obtain informed consent during a study that is granted by Human Subject Protection committee for a research institution for a protocol that is being reviewed by the Institutional Review Board. Sufficient SCDO:0005773 International Ethical Guidelines for Health-related Research Involving Humans, Fourth Edition. Geneva. Council for International Organizations of Medical Sciences (CIOMS); 2016. NCIT:C103270 Consent Waiver Waiver Of Informed Consent Waiver of the requirement of a signed consent form from potential participants or parents of children who are potential participants may be approved by a Research Ethics Committee if the research carries no more than minimal risk (i.e., risk that is no more likely and not greater than that attached to routine medical or psychological examination) and if the procedures to be used are only those for which signed consent forms are not customarily required outside the research context. Such waivers may also be approved when existence of a signed consent form would be an unjustified threat to the participant's confidentiality. Waiver of Consent NCIT:C103526 A 9-item scale using each of the 9 DSM-IV criteria with self-reported frequency of "0" (not at all) to "3" (nearly every day). One of the most widely used instruments to assess depression, PHQ-9 scores of 5, 10, 15, and 20 represent mild, moderate, moderately severe, and severe depression, respectively. Sufficient SCDO:0000870 Kroenke K, Spitzer R, Williams W. The PHQ-9: Validity of a brief depression severity measure. Journal of General Internal Medicine. 2001; 16: 606-616. NCIT:C103526 PHQ-9 PHQ01 Patient Health Questionnaire - 9 Item Patient Health Questionnaire-9 Patient Health Questionnaire-9 (PHQ-9) NCIT:C107564 Hemoglobin that has a nitric oxide bound to the cysteine at position 93 in the beta-globin chain. Sufficient SCDO:1000169 NCIT:C107564 S-Nitrosated Hemoglobin S-Nitrosohemoglobin S-Nitroso-Hemoglobin NCIT:C113340 The cessation of menstruation for six months or more in a female that is not pregnant, breastfeeding or menopausal. Sufficient SCDO:0001447 NCIT:C113340 Secondary Amenorrhea NCIT:C114300 Hemoglobin where the heme group has formed a stable complex with carbon monoxide (CO). This complex is produced after CO has been inhaled or as a byproduct of hemoglobin, protoporphyrin or dichloromethane catabolism. The heme-CO complex is approximately 200 times more stable than heme-oxygen complexes. Thus, high levels of carboxyhemoglobin in the circulation can lead to tissue hypoxia and death. Sufficient SCDO:1000168 NCIT:C114300 COHb Carboxyhemoglobin COHb NCIT:C114714 A severe hypersensitivity-like reaction occurring during dialysis due to exposure to the dialysis membrane. Sufficient SCDO:1000387 NCIT:C114714 Dialyzer Reaction Dialysis Membrane Reaction NCIT:C114717 A crack or break in a dialysis catheter caused by material weakness or mechanical compression. Sufficient SCDO:1000386 NCIT:C114717 Dialysis Catheter Fracture NCIT:C115199 Any heart or vascular disorder occurring as a consequence of injury to the cardiovascular system. Sufficient SCDO:1000390 NCIT:C115199 Cardiovascular Complication NCIT:C115224 Any disorder of the liver occurring as a consequence of injury to the liver parenchyma. Sufficient SCDO:1000382 NCIT:C115224 Liver Complication Hepatic Complication NCIT:C115319 Any eye disorder occurring as a consequence of injury to the eye. Sufficient SCDO:0000832 NCIT:C115319 Ophthalmologic Manifestations Ophthalmologic Complication NCIT:C116081 Any issue that arises as a consequence of a problem with a patient's dialysis access. Sufficient SCDO:1000391 NCIT:C116081 Dialysis Access Complication NCIT:C116161 A type of high-throughput, multiplex PCR method used to determine abnormal DNA copy number changes of up to 50 genomic DNA or RNA sequences with a single pair of PCR primers. It is frequently used in the detection of genetic aberrations in tumors, and can distinguish sequences differing in only a single nucleotide. Sufficient SCDO:0003929 NCIT:C116161 MLPA Multiplex Ligation-Dependent Probe Amplification NCIT:C116942 Failure to meet, or late achievement of developmental milestones. Can have many different causes, such as genetic causes (like Down syndrome), or complications of pregnancy and birth (like prematurity or infections). Often, however, the specific cause is unknown. Some causes can be easily reversed if caught early enough, such as hearing loss from chronic ear infections, or lead poisoning. Sufficient SCDO:0001293 http://www.med.umich.edu/yourchild/topics/devdel.htm NCIT:C116942 Developmental Delay NCIT:C118385 Tissue death resulting from an interruption to the blood supply. This is a synonym for osteonecrosis in our ontology (SCDO:0000841), which is controversial between different literature. Please check with a clinician if these two terms refer to the same condition. http://purl.obolibrary.org/obo/NCIT_C118385 Sufficient SCDO:0004832 NCIT:C118385 AVN deprecated-Avascular Necrosis true NCIT:C120254 A standardized tool designed to assess an individual's cognitive abilities. It consists of a battery of tests that allow an investigator to conduct a comprehensive cognitive evaluation of IQ. Life stage: Adolescent, Adult The Sickle Cell Disease Neurology, Quality of Life, and Health Services Working Group recognizes that there is an age overlap between the WAIS-IV and the Wechsler Intelligence Scale for Children-Fifth Edition (WISC-V). The Working Group recommends providers use their clinical judgment, consider the purpose of testing participants, and refer to the frequently asked questions section of the Pearson website for the WAIS-IV and the WISC-V for guidance on selecting an age-appropriate test for individuals. http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820501 PhenX protocol: Intelligence Scale - 16 to 90 years #820501 Sufficient SCDO:0000646 NCIT:C120254 WAIS-IV Wechsler Adult Intelligence Scale - Fourth Edition Wechsler Adult Intelligence Scale 4th Edition Wechsler Adult Intelligence Scale, Fourth Edition Wechsler Adult Intelligence Scale, Fourth Edition (WAIS-IV) Intelligence Scale - 16 to 90 years NCIT:C120255 A battery of tests that allow an investigator to conduct a comprehensive evaluation of a child or adolescent's cognitive ability. It consists of a core battery of subtests, which focus on five specific domains (verbal comprehension, processing speed, visual spatial, working memory, and fluid reasoning), as well as optional ancillary subtests. These ancillary subtests measure areas that are important to areas of academic achievement. Life stage: Child, Adolescent The Sickle Cell Disease Neurology, Quality of Life, and Health Services Working Group recognizes that there is an age overlap between the Wechsler Intelligence Scale for Children®-Fifth Edition (WISC-V) and Wechsler Preschool and Primary Scale of Intelligence-Fourth Edition (WPPSI-IV), as well as between the WISC-V and the Wechsler Adult Intelligence Scale, Fourth Edition (WAIS-IV). The Working Group recommends that providers use their clinical judgment, consider the purpose of testing participants, and refer to the frequently asked questions section of the Pearson website for WISC-V, WPPSI-IV, and WAIS-IV for guidance on selecting an age-appropriate test. http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820503 PhenX protocol: Intelligence Scale - 6 to 16 years 11 months #820503 Sufficient SCDO:0000648 NCIT:C120255 WISC-V Wechsler Intelligence Scale for Children-Fifth Edition Wechsler Intelligence Scale for Children-Fifth Edition (WISC-V) Intelligence Scale - 6 to 16 years 11 months NCIT:C120256 A standardized tool designed to assess the cognitive development in preschool and young children (up to age 7 years and 7 months). It consists of a battery of tests that allow an investigator to conduct a comprehensive evaluation of IQ. Life stage: Toddler, Child The Sickle Cell Disease Neurology, Quality of Life, and Health Services Working Group recognizes that there is an age overlap between the WPPSI-IV and the Bayley Scales of Infant and Toddler Development, Third Edition (Bayley-III) and between the WPPSI-IV and the Wechsler Intelligence Scale for Children-Fifth Edition (WISC-V). The Working Group recommends that providers use their clinical judgment, consider the purpose of testing participants, and refer to the frequently asked questions section of the Pearson website for the WPPSI-IV, Bayley-III, and the WISC-V for guidance on selecting an age-appropriate test. http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820502 PhenX protocol: Intelligence Scale - 2 years, 6 months to 7 years, 7 months #820502 Sufficient SCDO:0000647 NCIT:C120256 WPPSI-IV Wechsler Preschool & Primary Scale of Intelligence 4th Edition Wechsler Preschool and Primary Scale of Intelligenc-Fourth Edition Wechsler Preschool and Primary Scale of Intelligenc-Fourth Edition (WPPSI-IV) Wechsler Preschool and Primary Scale of Intelligence IV Intelligence Scale - 2 years, 6 months to 7 years, 7 months NCIT:C122920 An assessment tool designed to measure an individual's cognitive capabilities. It may be general or it may assess abilities in more discrete cognitive domains. Sufficient SCDO:0000645 NCIT:C122920 Intelligence Test Intelligence Scale NCIT:C122931 A diagnostic technique that uses pulsed Doppler ultrasound to both identify blood vessels in the brain and measure the velocity of blood flow through those vessels. It allows a more accurate estimation of stroke risk because it allows outlining of parenchymal structures and visualization of the examined vessels. http://purl.obolibrary.org/obo/NCIT_C122931 Sufficient SCDO:0000613 NCIT:C122931 TCDi Imaging Transcranial Doppler Ultrasonography NCIT:C123446 A continuous electrocardiographic (ECG) recording that utilizes one or more leads that both records and stores data directly to a device worn by the subject, such that the subject need not be restricted to a medical facility, and may be able to participate in their customary activities of daily living. http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C123446 Sufficient SCDO:0000281 NCIT:C123446 Continuous Ambulatory ECG NCIT:C123667 A standardized rating scale developed by Ziad Nasreddine in 1996 to screen for mild cognitive dysfunction and impairment. This instrument assesses the following cognitive domains: attention and concentration, executive functions, memory, language, visuoconstructional skills, conceptual thinking, calculations, and orientation PhenX protocol: Global Mental Status Screener - Adult #130701 Sufficient SCDO:1000335 NCIT:C123667 MOCA MOCA01 Montreal Cognitive Assessment Montreal Cognitive Assessment Functional Test Montreal Cognitive Assessment Questionnaire Global Mental Status Screener - Adult NCIT:C124059 A chest X-ray finding indicating the presence of a radio-opaque area in the lung. The opacification is caused by fluid or solid material within the airways or lung parenchyma. Described in the Tanzania guidelines as 'reduced air entry, increased tactile vocal fremitus, and dull percussion at lung bases, usually bilateral'. http://purl.obolibrary.org/obo/NCIT_C124059 Sufficient SCDO:0006222 NCIT:C124059 Air Space Opacificatio Air-Space Shadowing Airspace Consolidation Airspace Opacification Consolidation Pulmonary Consolidation NCIT:C124065 A measurement of the concentration of iron in the liver as an estimate of body iron load. http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C124065 Sufficient SCDO:0000555 NCIT:C124065 Hepatic Iron Liver Iron Liver Iron Concentration Hepatic Iron Concentration NCIT:C124475 A circumferential measurement of the largest part of the upper arm. http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C124475 Sufficient SCDO:0000758 NCIT:C124475 MUAC MUARMCIR Mid-Upper Arm Circumference Mid Upper Arm Circumference NCIT:C126120 Hemoglobin where the heme group has formed a reversible complex with oxygen (O2) in the lungs. This molecule is found in the systemic arteries and transports O2 from the lungs to the tissues where it is readily released. Sufficient SCDO:1000275 NCIT:C126120 HbO2 Oxyhemoglobin Oxygenated Hemoglobin NCIT:C126121 Hemoglobin containing a heme group that is not bound to oxygen (O2). This molecule is normally found in the systemic veins following transit through capillaries and release of O2 into the tissues. Excess deoxyhemoglobin can be associated with hypoxia. Sufficient SCDO:1000057 NCIT:C126121 Deoxyhemoglobin Deoxygenated Hemoglobin NCIT:C128326 An abscess within the abdomen. http://purl.obolibrary.org/obo/NCIT_C128326 Sufficient SCDO:0008079 NCIT:C128326 Intra-Abdominal Abscess NCIT:C129072 The persistence of substantial fetal hemoglobin production into adulthood, usually associated with hemoglobinopathies due to mutations in the alpha and/or beta chain of hemoglobin. Sufficient SCDO:0000560 NCIT:C129072 HPFH Hereditary Persistence of Foetal Haemoglobin This is a benign condition. Hereditary Persistence of Fetal Hemoglobin NCIT:C131682 A variant of sickle cell disease due to homozygosity of the E6V mutation, amino acid substitution of valine for glutamic acid in the sixth position of the beta chain, resulting in the production of hemoglobin S from both alleles. Sufficient SCDO:0000549 NCIT:C131682 Hb SS Disease Hb SS-Disease Hemoglobin SS Disease Homozygous Sickle Cell Disease SCA SS and S/Beta-Zero Thalassemia Severe SCD Sickle Cell Anemia Sickle Cell Disease SS Sickle Cell Hemoglobin S Disease Sickle Cell-SS Disease Sickle Cell Disease-SS NCIT:C133543 A humanized monoclonal immunoglobulin G1 anti-P-selectin antibody with vaso-protective and anti-vaso-occlusive properties. Upon administration, crizanlizumab binds to P-selectin and blocks its interaction with P-selectin glycoprotein ligand-1 (PSGL-1; SELPLG) on neutrophils and monocytes. P-selectin, a glycoprotein that functions as a cell adhesion molecule (CAM), translocates to the surface of activated endothelial cells and platelets, upon stimulation, where it binds to its ligand and mediates the rolling of platelets and neutrophils on activated endothelial cells. Therefore, blockade of p-selectin may inhibit platelet aggregation, maintain blood flow and minimize sickle cell-related pain crises (SCPC). Sufficient SCDO:1000380 NCIT:C133543 Adakveo SEG101 SelG1 Crizanlizumab NCIT:C141366 A rare autosomal recessive hemoglobinopathy, caused by the presence of two deltabeta globin fusion chains, which occurs due to a crossover between the delta (HBD) and beta globin (HBB) gene loci during meiosis. http://en.wikipedia.org/wiki/Hemoglobin_Lepore_syndrome Sufficient SCDO:0000538 NCIT:C141366 Hb Lepore Hb Lepore Syndrome Homozygous Hb Lepore Homozygous Hemoglobin Lepore Hemoglobin Lepore Syndrome NCIT:C142494 To maintain data by placing the data, or a copy of the data, onto an electronically accessible device for preservation (either in plain-text or encrypted format). Sufficient SCDO:1000420 NCIT:C142494 Data Storage NCIT:C142541 An independent group that comprises medical, scientific, and non-scientific members, and is tasked with the continuing review and approval of research, including clinical trials, with respect to the protocols, methods, and informed consent process to ensure the protection of the rights, safety, and wellbeing of participants. Sufficient SCDO:0009748 NCIT:C142541 Ethics Committee Human Subject Protection Committee REC Research Ethics Committee Research Ethics Committee NCIT:C142664 The interval of time during which subjects are to be enrolled in a clinical study. Sufficient SCDO:1000400 NCIT:C142664 Recruitment Period NCIT:C152089 An orally bioavailable modulator and stabilizer of sickle cell hemoglobin (HbS), with potential use in the treatment of sickle cell disease (SCD). Upon administration, voxelotor targets and covalently binds to the N-terminal valine of the alpha chain of HbS. This stabilizes HbS, thereby improving oxygen binding affinity. The binding of voxelotor to HbS prevents HbS polymerization, reduces sickling, decreases red blood cell (RBC) damage and increases the half-life of RBCs. This improves blood flow and decreases hemolytic anemia. Sufficient SCDO:1000381 NCIT:C152089 GBT-440 GBT440 Oxbryta Is an accepted therapy for adults and pediatric patients 12 years of age and older with sickle cell disease. Voxelotor NCIT:C15238 Application of genetic material (usually DNA) into cells in order to permanently correct an inherited disease or acquired disease. http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C15238 Sufficient SCDO:0001344 NCIT:C15238 DNA Therapy Gene Therapy NCIT:C15320 A plan detailing how a study will be performed in order to represent the phenomenon under examination, to answer the research questions that have been asked, and defining the methods of data analysis. Study design is driven by research hypothesis being posed, study subject/population/sample available, logistics/resources: technology, support, networking, collaborative support, etc. Review current sub-classes in light of and include relevant classes from "EDDA Study Designs Taxonomy" to be added as sub-classes. Sufficient SCDO:0001115 NCIT:C15320 Experiment Design Experimental Design Research Design STYPE Study Design NCIT:C154481 A patient-reported outcome measurement system designed to evaluate and monitor the physical, mental, and social well-being of adults with sickle cell disease. Cross-cultural adaptation underway in Brazil. ASCQ-Me's development using modern measurement theory facilitates cross cultural adaptation. PhenX protocol: Adult Sickle Cell Quality of Life Measurement Information System (ASCQ-Me) #820201 Self Clinic Patients (Adults with SCD) Spanish; Portuguese This measure can be used to track health status and treatment outcomes and understand the health care requirements of patients with chronic conditions, such as sickle cell disease (SCD). Rigor in development, using modern measurement theory and aligned with PROMIS measurement development. 18 years and older no Sufficient SCDO:0000027 Keller SD, Yang M, Treadwell MJ, Werner EM, Hassell KL (2014).Patient reports of health outcome for adults living with sickle cell disease: development and testing of the ASCQ-Me item banks. Health and Quality of Life Outcomes,12,125. NCIT:C154481 ASCQ-Me Adult Sickle Cell Quality of Life Measurement Information System Adult Sickle Cell Quality-of-Life Measurement Information System It includes questions that enable adults with SCD to describe their functioning and well-being. Its measures are available as 5 item short forms or can be administered as computer adaptive tests. Measures include: Pain Impact; Stiffness Impact (5-item short form); Sleep Impact; Social Functioning Impact; Emotional Impact; Pain Episodes; and Pain Frequency. Adult Sickle Cell Quality-of-Life Measurement Information System (ASCQ-Me) NCIT:C154865 An evaluation of the perfusion of blood through the brain. Sufficient SCDO:0000204 NCIT:C154865 Cerebral Blood Flow Assessment Cerebral Blood Flow Measurement Stroke Risk Test Cerebral Blood Flow Assay NCIT:C155310 A variant of sickle cell disease due to heterozygosity for hemoglobin S and hemoglobin D mutations. Patients present with the symptoms of sickle cell disease but the symptoms are less frequent and severe compared to patients with hemoglobin SS disease. Sufficient SCDO:0001060 NCIT:C155310 Haemoglobin S-D Disease Hb SD-Disease Hemoglobin S-D Disease Hemoglobin Sickle D Disease Sickle Cell Disease SD Sickle Cell Hemoglobin D Disease Sickle Cell-Haemoglobin D Disease Sickle Cell-Hemoglobin D Disease Sickle Cell Disease-SD NCIT:C155312 A pulmonary complication of sickle cell disease characterized by radiographic interstitial abnormalities and impaired pulmonary function. In severe cases, pulmonary hypertension is present. Restricive lung disease often associated with chest pain and hypoxemia. May also be associated with pulmonary hypertension. Sufficient SCDO:0001046 Powars et al 1988 Medicine (Baltimore), Knight-Madden et al 2010 Lung. NCIT:C155312 Sickle Cell Chronic Restrictive Lung Disease Sickle Cell Chronic Lung Disease NCIT:C155932 A clinician-assessed rating of psychological and social functioning in children ages six to seventeen that was developed by Shaffer et al. in 1983. The numerical scale, which is an adaptation of the adult Global Assessment Scale (GAS) developed by Endicott et al in 1976, is scored from 0 to 100 based on behaviors and life situations that are applicable to children. PhenX protocol: Global Mental Status Screener - Older Children and Adolescents #130703 Sufficient SCDO:1000334 NCIT:C155932 CGAS Children’s Global Assessment Scale Children’s Global Assessment Scale (CGAS) Global Mental Status Screener - Older Children and Adolescents NCIT:C156541 A person who is separated from their spouse, whether or not there is a legal arrangement. Sufficient SCDO:1000677 NCIT:C156541 Separated NCIT:C15709 The process of isolating and testing the DNA of an embryo or a person to detect the presence of genetic alterations or defects that may predispose to the future development of a disease or disorder. Note: "Genetic Test" is a SNOMED CT term. Include NCIT's "Presymptomatic Testing" as a sub-class? http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C15709 Sufficient SCDO:0000449 NCIT:C15709 Genetic Analysis Genetic Examination Genetic Test Genetic Testing NCIT:C15900 Therapy dealing with lifestyle management and includes: behavioral and dietary modifications, exercise, stress management, and addiction control. This therapy must be used as major adjunct to 'standard care' or be applied as alternative treatment to conventional medicine practices. Sufficient SCDO:1000006 NCIT:C15900 Lifestyle Therapy NCIT:C1643 An polyvalent vaccine used to prevent infection by the bacterium Streptococcus pneumoniae. Pneumococcal polyvalent vaccine contains highly purified capsular antigens from the 23 most prevalent or invasive pneumococcal types of Streptococcus pneumoniae to ensure cross-protection. Following vaccination, protective capsular type-specific antibody levels typically develop by the third week; serotype-specific antibody levels generally decline after 5-10 years. http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C1643&jump_to_nav=true Sufficient SCDO:0000915 NCIT:C1643 PPSV Pneumococcal Polysaccharide Vaccine Pneumococcal Polyvalent Vaccine Polyvalent Pneumococcal Vaccine NCIT:C164339 The date on which a diagnosis of disease was made. Sufficient SCDO:1000557 NCIT:C164339 Date of Diagnosis NCIT:C16453 A set of people with some shared element. The substance of shared element varies widely, from geography to a situation to interest to lives and values. The term is widely used to evoke sense of collectivity. Sufficient SCDO:0000266 NCIT:C16453 Community NCIT:C16495 The statistical characterization of human populations or segments of human populations (e.g., characterization by age, sex, race, or income). Sufficient SCDO:1000468 NCIT:C16495 Demographic Factors Demographics Demography Population Studies / Demography Demographic Factor NCIT:C16564 A social group characterized by a distinctive social and cultural tradition that is maintained from generation to generation. Members share a common history and origin and a sense of identification with the group. They have similar and distinctive features in their lifestyle habits and shared experiences. They often have a common genetic heritage which may be reflected in their experience of health and disease. Include other Ethnic groups that are sub-classes of "Ethnic Group" in ERO. http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C16564 Sufficient SCDO:0001298 NCIT:C16564 Ethnic Origin Ethnic Origins Ethnicity Ethnic Group NCIT:C16567 Activity that requires physical or mental exertion, especially when performed to develop or maintain fitness. Sufficient SCDO:0001305 NCIT:C16567 Exercise NCIT:C16576 A person who belongs to the sex that normally produces ova. The term is used to indicate biological sex distinctions, or cultural gender role distinctions, or both. Sufficient SCDO:1000560 NCIT:C16576 Female NCIT:C16612 A functional unit of heredity which occupies a specific position on a particular chromosome and serves as the template for a product that contributes to a phenotype or a biological function. Sufficient SCDO:1000359 NCIT:C16612 Gene NCIT:C16632 Any demarcated area of the Earth; may be determined by both natural and human boundaries. Sufficient SCDO:1000367 NCIT:C16632 Geographic Location Geographic Region Geographic Area NCIT:C16676 The red respiratory protein of erythrocytes, consisting of approximately 3.8% heme and 96.2% globin (64.5 KD), which as oxyhemoglobin (HbO2) transports oxygen from the lungs to the tissues where the oxygen is readily released and HbO2 becomes Hb. Sufficient SCDO:0009453 NCIT:C16676 Hb Hgb Hemoglobin NCIT:C16723 Laboratory test involving interaction of antigens with specific antibodies. Sufficient SCDO:0000617 NCIT:C16723 Immunoassay Immunological Laboratory Method Immunology Test Immunological Assay NCIT:C16779 A systematic means of communicating by the use of sounds, symbols, or gestures. http://purl.obolibrary.org/obo/NCIT_C16779 Sufficient SCDO:0005364 NCIT:C16779 Language NCIT:C16809 Imaging that uses radiofrequency waves and a strong magnetic field rather than x-rays to provide amazingly clear and detailed pictures of internal organs and tissues. The technique is valuable for the diagnosis of many pathologic conditions, including cancer, heart and vascular disease, stroke, and joint and musculoskeletal disorders. http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C16809 Sufficient SCDO:0000708 NCIT:C16809 MIR Scan MRI MRT Magnetic Resonance Imaging Scan Magnetic Resonance Tomography NMR Imaging NMRI Nuclear Magnetic Resonance Imaging Magnetic Resonance Imaging NCIT:C168823 The year when a diagnosis was assigned to an individual's condition. Sufficient SCDO:1000567 NCIT:C168823 Year of Diagnosis NCIT:C17004 The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site to large nucleotide sequences visible at a chromosomal level. Sufficient SCDO:0004047 NCIT:C17004 Genetic Polymorphism NCIT:C17047 The subjective measurement of an individual's sense of well-being and ability to enjoy life. The concept holds varying meanings for different people and may evolve over time. For some individuals it implies autonomy, empowerment, capability, and choice; for others, security, social integration, or freedom from stress or illness. Sufficient SCDO:0000949 NCIT:C17047 Health Related Quality of Life QOL Quality of Life NCIT:C17049 An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation within a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution. Different relevant racial groups need to be recorded. Perhaps as sub-classes of this class? The PhenX protocol is U.S. specific. Is there one relevant to the African setting? http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C17049 Sufficient SCDO:0000962 NCIT:C17049 Racial Group Race NCIT:C17230 A technique in which high-frequency sound waves are bounced off internal organs and the echo pattern is converted into a 2 dimensional picture of the structures beneath the transducer. http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C17230 Sufficient SCDO:0000614 NCIT:C17230 Immaging by Ultrasonography Ultrasonography Ultrasound Ultrasound Imaging Ultrasound Test NCIT:C17241 Laboratory analysis of urine, commonly used to aid in the diagnosis of disease or to detect the presence of a specific substance. It involves examination of the urine by physical or chemical means as well as microscopic examination that helps to screen for urinary tract infections, renal disease, and diseases of other organs, that result in abnormal metabolites (break-down products) appearing in the urine. Other urine tests to be added as sub-classes? There are many in the NCIT. Sufficient SCDO:0001216 NCIT:C17241 Urinalysis Urine Analysis Urine Test NCIT:C173396 The rate of blood flow through the cerebral arteries. Sufficient SCDO:0000205 NCIT:C173396 CBF Velocity CBFV Transcranial Doppler Velocity Cerebral Blood Flow Velocity NCIT:C17357 The assemblage of properties that distinguish people on the basis of the societal roles expected for the two sexes. Sufficient SCDO:0001341 NCIT:C17357 Gender NCIT:C17655 An account of all reproductive events and problems a person has experienced. An important aggregate factor in epidemiological studies of women's health. The concept usually includes the number and timing of pregnancies and their outcomes, the incidence of breast feeding, and may include age of menarche and menopause, regularity of menstruation, fertility, gynecological or obstetric problems, or contraceptive usage. Sufficient SCDO:1000346 NCIT:C17655 Reproductive History NCIT:C17873 Having to do with the physical, psychological, cognitive, and social consequences of disease, including stigmatization of persons affected. http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C17873 Sufficient SCDO:0000939 NCIT:C17873 Psychosocial Effects Psychosocial Effects/Treatment Psychosocial Effect NCIT:C18133 A single base pair substitution that alters the genetic code in a way that produces an amino acid that is different from the usual amino acid at that position. Some missense mutations will alter the function of the protein. Sufficient SCDO:0004314 NCIT:C18133 Missense Mutation NCIT:C18772 A record of a patient's background regarding health and the occurrence of disease events of the individual. In addition, personal medical history may be a variable in epidemiologic studies. Sub-classes in NCIT to be added here. http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C18772 Sufficient SCDO:0000891 NCIT:C18772 General Medical History Medical History PMH Past Medical History Personal Medical History NCIT:C19228 An instrument used to measure an event involving emission, absorption, or refraction of light. http://purl.obolibrary.org/obo/NCIT_C19228 Sufficient SCDO:0000837 NCIT:C19228 Optical Instrument NCIT:C19296 Any rearrangement to the genomic content that results in the loss of one or more nucleotides of DNA. Deletions are generally irreversible rearrangements. They may alter the reading frame of a gene, or may result in loss of large chromosomal regions. http://purl.obolibrary.org/obo/NCIT_C19296 Sufficient SCDO:0001371 NCIT:C19296 Deletion Abnormality Deletion Mutation NCIT:C19332 The distinguishing qualities or prominent aspects of an individual person. Populate this class with demographic terms from PhenX and elsewhere. Some terms will be duplicated in QoL. -- -- Add these from PhenX?: -- - Acculturation -- - Residential History -- -- Also look at other sub-classes in NCIT. http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C19332 Sufficient SCDO:0000890 NCIT:C19332 Subject Characteristics Personal Attribute NCIT:C19771 Analysis of the RNA expression pattern in a tissue sample using molecular techniques. Sufficient SCDO:0000768 NCIT:C19771 Expression Profiling Molecular Fingerprinting Molecular Profiling Molecular Profiling Assay NCIT:C20197 A person who belongs to the sex that normally produces sperm. The term is used to indicate biological sex distinctions, cultural gender role distinctions, or both. Sufficient SCDO:1000559 NCIT:C20197 Male NCIT:C20629 A point mutation occurring within the protein-coding region of a gene, and which codes for the same amino acid as expected. Sufficient SCDO:0005439 NCIT:C20629 Exon Synonymous Mutation Exonic Synonymous Mutation Synonymous Mutation Silent Mutation NCIT:C20711 This gene plays a role in transcriptional regulation and is involved in several signal transduction pathways. Sufficient SCDO:1000393 NCIT:C20711 SP1 Sp1 Transcription Factor Gene SP1 Gene NCIT:C25150 How long something has existed; elapsed time since birth. Could add many sub-classes of "Age" from NCIT. http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25150 Sufficient SCDO:0000030 NCIT:C25150 Aged Chronological Age Postnatal Age Age NCIT:C25191 A word or group of words indicating the identity of a person usually consisting of a first (personal) name and a last (family) name with an optional middle name. In some cultural traditions the family name comes first. Sufficient SCDO:1000859 NCIT:C25191 Contact Name Individual's Name Name Name of Person Person.name Person Name NCIT:C25298 The maximum pressure exerted into the systemic arterial circulation during the contraction of the left ventricle of the heart. Sufficient SCDO:1000892 NCIT:C25298 SYSBP Systolic Pressure systolic bp Systolic Blood Pressure NCIT:C25299 The minimum pressure exerted into the systemic arterial circulation during cardiac ventricular relaxation and filling. Sufficient Vital Signs 6 SCDO:1000893 NCIT:C25299 DIABP Diastolic Pressure Diastolic Blood Pressure NCIT:C25460 Permission to do something. http://purl.obolibrary.org/obo/NCIT_C25460 Sufficient SCDO:0001466 NCIT:C25460 Consent NCIT:C25464 A collective generic term that refers here to a wide variety of dependencies, areas of special sovereignty, uninhabited islands, and other entities in addition to the traditional countries or independent states. http://purl.obolibrary.org/obo/NCIT_C25464 Sufficient SCDO:0004140 NCIT:C25464 deprecated Country true NCIT:C25474 A collection or single item of factual or reported information, derived from measurement or research, from which conclusions may be drawn. Sufficient SCDO:0006670 NCIT:C25474 Data NCIT:C258 Substances naturally produced by microorganisms or their derivatives that selectively target microorganisms not humans. Antibiotics kill or inhibit the growth of microorganisms by targeting components of the microbial cell absent from human cells, including bacterial cell walls, cell membrane, and 30S or 50S ribosomal subunits. These substances are used in the treatment of bacterial and other microbial infections. http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C258 Sufficient SCDO:0000059 NCIT:C258 Antibiotic Agents Antibiotic Drug Antibiotic Drugs Antibiotics Antimicrobial Antimicrobial Agent Antibiotic NCIT:C26548 A protein, RNA or a complex that contains proteins and/or RNA. If additional gene products are included in the future, they can be categorised according to those below this term in the "National Cancer Institute Thesaurus" (NCIT) http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C26548 Sufficient SCDO:0001343 NCIT:C26548 Genome Encoded Entity Gene Product NCIT:C26702 Lack of coordination of muscle movements resulting in the impairment or inability to perform voluntary activities. Causes include peripheral nerve disorders, posterior column injuries, cerebral and cerebellar disorders, basal ganglia disorders, and thalamic disorders. Perhaps add "Cerebellar Ataxia" subclass? Sufficient SCDO:0000087 NCIT:C26702 Ataxia NCIT:C27088 Abnormally high level of bilirubin in the blood. Excess bilirubin is associated with jaundice. Sufficient SCDO:0003118 NCIT:C27088 High Blood Bilirubin Levels Hyperbilirubinemia NCIT:C27222 A balloon type pouch or bulge in the wall of a cerebral blood vessel. Sufficient SCDO:0000202 NCIT:C27222 Brain Aneurysm Cerebral Artery Aneurysm Dilatation of the Cerebral Artery Intracranial Aneurysm Cerebral Aneurysm NCIT:C28407 System of classification based on nation from which a person originates, regardless of the nation in which he/she currently resides. Include list of nations below. http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C28407 Sufficient SCDO:0000792 NCIT:C28407 Birth Country Country of Birth Country of Origin National Origin NCIT:C28421 The totality of characteristics of reproductive structure, functions, phenotype, and genotype, differentiating the male from the female organism. Sufficient SCDO:1000671 NCIT:C28421 Participant Sex Participant's Sex Respondent's Sex Sex of Participant Sex NCIT:C28516 A severe acute inflammatory response affecting the hands and feet of individuals with sickle cell disease, sickle cell-hemoglobin C disease or sickle cell-beta-thalassemia. It is caused by vaso-occlusive episodes leading to ischemia and finally infarction of the distal portions of the extremities. Clinical signs of pain, swelling and tenderness of digits usually begin in early childhood and may be the initial manifestations of sickle cell anemia. Clinical course is self-limited with instances typically lasting a few weeks and occurring during sickling crises. An initial episode before the age of 1 strongly correlates with a more severe disease course. http://purl.obolibrary.org/obo/NCIT_C28516 Sufficient SCDO:0000477 NCIT:C28516 Sickle Cell Dactylitis NCIT:C2890 An acute infectious disorder caused by gram positive or gram negative bacteria. Representative examples include pneumococcal, streptococcal, salmonella and meningeal infections. Perhaps use as Disease Modifier? http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C2890 Sufficient SCDO:0000100 NCIT:C2890 Bacterial Infection NCIT:C2905 Increase in the number of hematopoietic cells in the bone marrow. It may involve all or individual hematopoietic cell lines. http://purl.obolibrary.org/obo/NCIT_C2905 Sufficient SCDO:0007438 NCIT:C2905 Hyperplasia of Bone Marrow Marrow Hyperplasia Bone Marrow Hyperplasia NCIT:C29091 A non-infectious mixture containing recombinant hepatitis B surface antigen (HBsAg) in a liquid vehicle. Immunization with the hepatitis B vaccine induces the formation of specific anti-hepatitis B antibodies and an active immunity against hepatitis B infection. http://purl.obolibrary.org/obo/NCIT_C29091 Sufficient SCDO:0008062 NCIT:C29091 ENGERIX-B Hepatitis B Vaccine (Recombinant) RECOMBIVAX HB Recombinant Hepatitis B Vaccine Hepatitis B Vaccine NCIT:C29107 A sterile liquid preparation infused into a vein. IV fluid is prescribed as a replacement of fluid, electrolytes, calories, vitamins, and other nutritional substances. In addition, IV fluids are used to administer blood products and medications such as chemotherapy. Examples of IV fluids include Normal Saline, Ringers Solution, and Lactated Ringers Solution. http://purl.obolibrary.org/obo/NCIT_C29107 Sufficient SCDO:0005247 NCIT:C29107 Intravenous Fluid IV fluids NCIT:C2959 Any disease or disorder that occurs during the course of, or because of, another disease, treatment, or procedure. Sufficient SCDO:1000384 NCIT:C2959 Complications Medical Complication Complication NCIT:C29719 A record of an individual's background in regard to smoking tobacco. This would include such factors as start date, end date (if applicable), number of cigarette smoked, attempts to quit, and others. http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C29719 Sufficient SCDO:0001081 NCIT:C29719 Tobacco Smoking History Smoking History NCIT:C30142 An account of all experiences related to the receipt of blood, WBC, platelets, and/or other blood components. Sufficient SCDO:0000569 NCIT:C30142 Transfusion History History of Transfusion NCIT:C3245 An infection caused by a fungus. Sufficient SCDO:1000349 NCIT:C3245 Fungal Infection NCIT:C3439 Any disease caused by a virus. Perhaps use as Disease Modifier? Add these sub-classes: Hepatitis C Infection (term in NCIT) Hepatitis B Infection (term in NCIT) HIV Infection (term in NCIT) http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C3439 Sufficient SCDO:0001233 NCIT:C3439 Viral Disease Virus Disease Viral Infection NCIT:C34465 An acute or chronic inflammation involving the gallbladder wall. It may be associated with the presence of gallstones. http://purl.obolibrary.org/obo/NCIT_C34465 Sufficient SCDO:0007856 NCIT:C34465 Cholecystitis NCIT:C34887 A sensation of discomfort secondary to surgery. Sufficient SCDO:1000451 NCIT:C34887 Perioperative Pain Post Surgery Pain Post-Operative Pain Postoperative Pain Peri-Operative Pain NCIT:C34941 The co-occurrence of pregnancy and a disease. The disease may precede or follow conception and it may or may not have a deleterious effect on the pregnant woman or fetus. Sufficient SCDO:1000399 NCIT:C34941 Complication Related to Pregnancy Pregnancy Complication NCIT:C35069 An inherited blood disorder characterized by a decreased synthesis of one of the polypeptide chains that form hemoglobin. Anemia results from this abnormal hemoglobin formation. Sufficient SCDO:0001144 NCIT:C35069 Thalassemia NCIT:C35146 Cholecystitis that is persistent and long-standing. http://purl.obolibrary.org/obo/NCIT_C35146 Sufficient SCDO:0009201 NCIT:C35146 Chronic Cholecystitis NCIT:C35152 Acute inflammation of the gallbladder. http://purl.obolibrary.org/obo/NCIT_C35152 Sufficient SCDO:0008927 NCIT:C35152 Acute Cholecystitis NCIT:C35372 Acute infection of the bile ducts caused by bacteria ascending from the small intestine. http://purl.obolibrary.org/obo/NCIT_C35372 Sufficient SCDO:0008766 NCIT:C35372 Ascending Cholangitis NCIT:C35447 Necrotic changes in the bone tissue of the femoral head due to interruption of blood supply. Add description. -- See HPO term "Avascular necrosis of the capital femoral epiphysis". -- -- Perhaps add "Bone decompression by drilling" to therapeutics and link to it with "is treated with http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C35447 Sufficient SCDO:0000842 NCIT:C35447 Avascular Necrosis of Femoral Head Avascular Necrosis of the Capital Femoral Epiphysis Avascular Necrosis of the Femoral Head Avascular Necrosis of the Head of Femur ONFH Osteonecrosis of the Femoral Head NCIT:C3671 Damage inflicted on the body as the direct or indirect result of an external force, with or without disruption of structural continuity. Sufficient SCDO:1000435 NCIT:C3671 Trauma Wound Injury NCIT:C38060 A test performed by an ophthalmologist or optometrist assessing vision and ability to focus on and discern objects, as well as other tests and examinations pertaining to the eyes. http://purl.obolibrary.org/obo/NCIT_C38060 Sufficient SCDO:0001313 NCIT:C38060 Eye Exam Eye Examination NCIT:C38085 A non-invasive method that provides estimates of arterial oxyhemoglobin saturation by utilizing selected wavelengths of light to determine the saturation of oxyhemoglobin. Sufficient SCDO:1000351 NCIT:C38085 Pulse Oximetry NCIT:C38141 An active immunizing agent used to prevent infection by the bacterium Streptococcus pneumoniae. Pneumococcal 7-valent conjugate vaccine consists of a solution of saccharides of the capsular antigens of Streptococcus serotypes 4, 6B, 9V, 14, 18C, 19F, and 23F individually conjugated to diphtheria CRM 197 protein. http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C38141 Sufficient SCDO:0000911 NCIT:C38141 7 Valent PncOMPC Vaccine 7-Valent PncOMPC Vaccine Heptavalent Pneumococcal Conjugate Vaccine PCV 7 PCV7 Vaccine Pneumococcal 7-Valent Conjugate Vaccine (Diphtheria CRM197 Protein) Prevenar Prevnar Seven Valent Pneumococcal PS Meningococcal OMPC Conjugate Vaccine Seven-Valent Pneumococcal PS-Meningococcal OMPC Conjugate Vaccine Pneumococcal 7-Valent Conjugate Vaccine NCIT:C3833 Without clinical signs or indications that raise the possibility of a particular disorder or dysfunction. Sufficient SCDO:0004802 NCIT:C3833 No Symptoms Asymptomatic NCIT:C38698 An increase in the viscosity of blood resulting from an increase in the proportion of cellular elements of the blood, a change in the mechanical properties of the cellular elements of the blood, and/or an alteration in plasma viscosity. http://purl.obolibrary.org/obo/NCIT_C38698 Sufficient SCDO:0002771 NCIT:C38698 Blood Hyperviscosity Hypercoagulability Thrombophilia Hyperviscosity NCIT:C3890 A decrease in the amount of oxygen in the body. Symptoms range from mild (impaired judgment, memory loss, impaired motor coordination) to severe (seizures and coma). In SCD patients, this is considered as saturated oxygen < 95% on air. Have merged the definition of hypoxia from NCIT and the Tanzanian Management Guidelines. Not sure if the SaO2 value is specific to SCD patients - please get a clinician to review. This is a symptom of acute chest syndrome. SCD Management guidelines - Tanzania Sufficient SCDO:0004183 NCIT:C3890 Hypoxia NCIT:C39547 The probability of benefit to individuals in a defined population from a medical technology applied for a given medical problem under ideal conditions of use. Efficacy is a measure of effect of therapy among appropriate patients in whom treatment is tolerated and effectively administered, under the condition of sufficient patients' compliance, usually determined in randomized trials. Sufficient SCDO:1000156 NCIT:C39547 Clinical Efficacy Treatment Efficacy NCIT:C39796 The philosophical study of moral values and rules. Ethics is a general term for what is often described as the "science of morality". The Western tradition of ethics is sometimes called moral philosophy. This is one of the three major branches of philosophy, alongside metaphysics and logic. http://purl.bioontology.org/ontology/MESH/D004989 Sufficient SCDO:0300001 NCIT:C39796 Moral Philosophy Natural Law Ethics NCIT:C40438 The BDI-II is the most widely used instrument for measuring depression. It consists of 21 items to assess the intensity of depression in clinical and normal patients. Each item is a list of four statements arranged in increasing severity about a particular symptom of depression, and rated on a scale of 0 to 3. Beck A.T., Ward C. H., Mendelson M., Mock J., & Erbaugh J. (1961) An inventory for measuring depression. Archives of General Psychiatry, 4, 561-571. Multiple countries and cultural groups Self Clinic Patients Spanish 13 years and older yes Sufficient SCDO:0000103 NCIT:C40438 BDI-II Beck Depression Inventory Beck Depression Inventory-II Beck Depression Inventory-II (BDI-II) NCIT:C40978 A sequence of decimal digits (0-9) that is used for identifying a destination telephone line or other device in a telephone network. Sufficient SCDO:1000881 NCIT:C40978 Phone Phone Number Telephone Telephone Number NCIT:C41129 An area or portion of something with more or less definite boundaries designed or specified according to some established biological, administrative, economic, demographic, etc. criteria. It didn't have sense to have this term as a sub-class of "Major Area", which has also been deprecated. http://purl.obolibrary.org/obo/NCIT_C41129 Sufficient SCDO:0006934 NCIT:C41129 deprecated Region true NCIT:C42559 A unit of temperature of the temperature scale designed so that the freezing point of water is 0 degrees and the boiling point is 100 degrees at standard atmospheric pressure. The current official definition of the Celsius sets 0.01 C to be at the triple point of water and a degree to be 1/273.16 of the difference in temperature between the triple point of water and absolute zero. One degree Celsius represents the same temperature difference as one Kelvin. Sufficient SCDO:1000713 NCIT:C42559 C Celsius Celsius Degree Celsius Temperature Degree C Degree Centigrade Degrees C Degrees Celsius Degree Celsius NCIT:C43646 An association is a non-hierarchical, named relationship between a source and target concept that does not affect classification and is not inherited by child concepts during classification. Associations are bidirectional and have a stated inverse. Unlike roles, associations do not have a domain or range. Sufficient SCDO:0005031 NCIT:C43646 Association NCIT:C48660 Determination of a value is not relevant in the current context. Sufficient SCDO:1000770 NCIT:C48660 Not Applicable NA NCIT:C49131 A diagnostic test used to examine and define microscopic tissue structure, composition, or etiology. The test results are often used by a clinician to diagnose disease or disordered function. Sufficient SCDO:0004740 NCIT:C49131 Histologic Test Diagnostic Histology Test NCIT:C49674 The number of breaths (inhalation and exhalation) taken per minute time. Sufficient SCDO:1000716 NCIT:C49674 Breaths/Minute bpm breaths/min {BREATHS}/min {breaths}/min Breaths per Minute NCIT:C50474 Abnormal decrease of rate of breathing. Sufficient SCDO:1000293 NCIT:C50474 Decreased Respiratory Rate Bradypnea NCIT:C50767 Abnormal increase of rate of breathing. Sufficient SCDO:1000347 NCIT:C50767 Fast Breathing Increased Respiratory Rate Tachypnea NCIT:C50791 A bacterial infectious process affecting any part of the urinary tract, most commonly the bladder and the urethra. Symptoms include urinary urgency and frequency, burning sensation during urination, lower abdominal discomfort, and cloudy urine. http://purl.obolibrary.org/obo/NCIT_C50791 Sufficient SCDO:0007744 NCIT:C50791 Urinary Tract Infection NCIT:C51677 Removal of tissue from the liver for microscopic examination. Use relevant object property to link to "Elevated Hepatic Iron Concentration". http://purl.obolibrary.org/obo/NCIT_C51677 Sufficient SCDO:0000693 NCIT:C51677 Liver Biopsy NCIT:C51773 Indicates a person currently joined in a legally binding matrimonial union. Classify common law marriage as married. Includes married couples living together and not living together. Sufficient SCDO:1000674 NCIT:C51773 Married Status Married NCIT:C51774 Indicates a person who has never been married or whose marriages have been annulled. Sufficient SCDO:1000678 NCIT:C51774 Never Been Married/Annulled Never Married Never Married Status Never Been Married NCIT:C51775 Indicates a person who is no longer married because of the death of his/her spouse and has not remarried. Sufficient SCDO:1000675 NCIT:C51775 Widowed Status Widowed NCIT:C51776 Indicates a person whose marriage has been legally dissolved and has not remarried. Sufficient SCDO:1000676 SCDO (Jade Hotchkiss) NCIT:C51776 Divorced NCIT:C519 A broad-spectrum aminoglycoside antibiotic produced by fermentation of Micromonospora purpurea or M. echinospora. Gentamicin is an antibiotic complex consisting of four major (C1, C1a, C2, and C2a) and several minor components. This agent irreversibly binds to the bacterial 30S ribosomal subunit. Specifically, this antibiotic is lodged between 16S rRNA and S12 protein within the 30S subunit. This leads to interference with translational initiation complex, misreading of mRNA, thereby hampering protein synthesis and resulting in bactericidal effect. Aminoglycosides are mostly ineffective against anaerobic bacteria, fungi and viruses. http://purl.obolibrary.org/obo/NCIT_C519 Sufficient SCDO:0001259 NCIT:C519 Garamicin Garamycin Genoptic Genoptic S.O.P. Gentamycin Gentamycin Complex U-Gencin Gentamicin NCIT:C51993 Administration of antibiotics with the intent of preventing bacterial infection. http://purl.obolibrary.org/obo/NCIT_C51993 Sufficient SCDO:0006790 NCIT:C51993 Is recommended, particularly up to the age of 5 years, to prevent bacterial infections in SCD patients. Antibiotic Prophylaxis NCIT:C52009 A prenatal diagnostic procedure in which a small sample of amniotic fluid is removed from the uterus by a needle inserted into the abdomen. This procedure is used to detect various genetic abnormalities in the fetus and/or the sex of the fetus. http://purl.obolibrary.org/obo/NCIT_C52009 Sufficient SCDO:0000048 NCIT:C52009 Amniotic Fluid Testing Amniocentesis NCIT:C561 A propionic acid derivate and nonsteroidal anti-inflammatory drug (NSAID) with anti-inflammatory, analgesic, and antipyretic effects. Ibuprofen inhibits the activity of cyclo-oxygenase I and II, resulting in a decreased formation of precursors of prostaglandins and thromboxanes. This leads to decreased prostaglandin synthesis, by prostaglandin synthase, the main physiologic effect of ibuprofen. Ibuprofen also causes a decrease in the formation of thromboxane A2 synthesis, by thromboxane synthase, thereby inhibiting platelet aggregation. Sufficient SCDO:0000606 http://www.drugbank.ca/drugs/DB01050 NCIT:C561 2-[4-(2-methylpropyl)phenyl]propanoic acid Advil Ibuprophen Motrin Ibuprofen NCIT:C61797 A cyclohexanone derivative with analgesic and anesthetic properties. Although its mechanism of action is not well understood, ketamine appears exerts complex pharmacological actions including inhibition of biogenic amine uptake, binding to opioid receptors, and inhibition of N-methyl D-aspartate (NMDA) receptors. Because of the involvement of spinal NMDA receptors in the process of central sensitization, this agent may reduce pain perception and induce sedation. Sufficient SCDO:1000450 NCIT:C61797 Ketamine NCIT:C62005 A derivative of dibenzocycloheptadiene and a tricyclic antidepressant. Amitriptyline inhibits the re-uptake of norepinephrine and serotonin by the presynaptic neuronal membrane in the central nervous system (CNS), thereby increasing the synaptic concentration of norepinephrine and serotonin. Due to constant stimulation to these receptors, amitriptyline may produce a downregulation of adrenergic and serotonin receptors, which may contribute to the antidepressant activity. Used to treat neuropathic pain http://purl.obolibrary.org/obo/NCIT_C62005 Sufficient SCDO:0004190 NCIT:C62005 Amitriptyline NCIT:C62198 A point mutation occurring within the protein-coding region of a gene, and which codes for a stop that can truncate the protein. Sufficient SCDO:0003789 NCIT:C62198 Premature Termination Abnormality Premature Termination Mutation Nonsense Mutation NCIT:C62200 A small scale mutation caused by the substitution of a single nucleotide for another nucleotide. http://purl.obolibrary.org/obo/NCIT_C62200 Sufficient SCDO:0001372 NCIT:C62200 Point Mutation NCIT:C63547 A way of denoting the collective genotype of a number of closely linked loci on a chromosome. Sufficient SCDO:0007716 NCIT:C63547 Haplotype NCIT:C64387 A unit of concentration (molarity unit) equal to one millimole of solute per liter of solution. Sufficient SCDO:1000899 NCIT:C64387 Millimolar mM mmol/L Millimole per Liter NCIT:C64572 A metric unit of mass concentration defined as the concentration of one gram of a substance per unit volume of the mixture equal to one cubic meter. The concept also refers to the metric unit of mass density (volumic mass) defined as the density of a substance which mass equal to one gram occupies the volume of one cubic meter. Sufficient SCDO:1000505 NCIT:C64572 Gram per Cubic Meter Microgram per Milliliter Microgram/Milliliter Milligram per Cubic Decimeter Milligram per Liter Nanogram per Microliter g/m3 gram(s)/cubic meter gram/cubic meter mcg/mL mg/L mg/dm3 mg/l microgram per milliliter microgram per millilitre microgram(s)/millilitre microgram/millilitre milligram per liter milligram(s)/litre ng/uL ug/mL ug/ml µg/mL microgram per millilitre NCIT:C64625 A 3-isobutyl derivative of gamma-amino butyric acid (GABA) with anti-convulsant, anti-epileptic, anxiolytic, and analgesic activities. Although the exact mechanism of action is unknown, pregabalin selectively binds to alpha2delta (A2D) subunits of presynaptic voltage-dependent calcium channels (VDCCs) located in the central nervous system (CNS). Binding of pregabalin to VDCC A2D subunits prevents calcium influx and the subsequent calcium-dependent release of various neurotransmitters, including glutamate, norepinephrine, serotonin, dopamine, and substance P, from the presynaptic nerve terminals of hyperexcited neurons; synaptic transmission is inhibited and neuronal excitability is diminished. Pregabalin does not bind directly to GABA-A or GABA-B receptors and does not alter GABA uptake or degradation. http://purl.obolibrary.org/obo/NCIT_C64625 Sufficient SCDO:0008454 NCIT:C64625 3-(Aminomethyl)-5-methyl-hexanoic Acid 3-Isobutyl GABA CI 1008 Lyrica PD 144723 Pregabalin NCIT:C64783 A unit of mass concentration defined as the concentration of one gram of a substance per unit volume of the mixture equal to one deciliter (100 milliliters). The concept also refers to the metric unit of mass density (volumic mass) defined as the density of substance which mass equal to one gram occupies the volume one deciliter. Sufficient SCDO:1000620 NCIT:C64783 Gram per Deciliter Gram/Deciliter g/dl gram per deciliter g/dL NCIT:C67015 A unit of mass concentration defined as the concentration of one milligram of a substance in unit volume of the mixture equal to one cubic deciliter or 100 cubic centimeters. It is also a unit of mass density (volumic mass) defined as the density of substance which mass equal to one milligram occupies the volume one cubic deciliter or 100 cubic centimeters. Sufficient SCDO:1000646 NCIT:C67015 Milligram per Deciliter Milligram/Deciliter mg/dl mg/dL NCIT:C67244 A unit of cell concentration expressed as a number of cells in thousands per unit volume equal to one microliter. Sufficient SCDO:1000511 NCIT:C67244 1000 cells/µL 10E3 Cells/uL 10^3 Cells/uL 10^3{Cells}/uL Thousand Cells per Microliter Thousand Cells/cu mm; thousand cells per microliter thousand cells/µL thousands/µL thousand cells per microliter NCIT:C67251 A unit of cell concentration expressed as a number of cells in millions per unit volume equal to one microliter. Sufficient SCDO:1000504 NCIT:C67251 10E6 cells/uL 10^6 Cells/uL 10^6{Cells}/uL Million Cells per Microliter Million Cells/cu mm million cells per microliter million cells per microlitre million cells/µL million cells per microliter NCIT:C67376 Unit of arbitrary substance concentration (biologic activity concentration) defined as the concentration of one international unit per one liter of the system volume. Sufficient SCDO:1000658 NCIT:C67376 IE/L International Unit per Liter International Unit per Litre International Unit/Liter International Unit/Litre Microinternational Unit per Microliter Milliinternational Unit per Milliliter IU/L NCIT:C68615 The calendar date on which a person was born. Sufficient SCDO:1000544 NCIT:C68615 BD DOB Date of Birth Birth Date NCIT:C69256 A unique identifier for a subject in a study. Sufficient SCDO:1000469 NCIT:C69256 Participant ID Participant Identifier Participant Number Research Subject ID Subject ID Subject Identification Code Subject Identifier Subject UID Subject Unique Identifier Subject's Unique Identifier Subject.identifier SubjectIdentifier USUBJID Unique Subject Identifier The unique identification of a subject in a specified context. NOTE(S): This class is a resolution of the requirement for noting the type of an identifier which is not handled by the purely technical HL7 II data type.; A unique symbol that establishes identity of the subject. EXAMPLE(S): study subject number 7 on a specific study OTHER NAME(S): NOTE(S):; Unique Identifier of patient or fetus who is the subject of observations.; The unique identification of a subject in a specified context. Subject Unique Identifier NCIT:C70731 A unique identifier assigned to each clinical trial subject to protect the subject's identity and used in lieu of the subject's name when the investigator reports adverse events and/or other trial-related data. http://purl.obolibrary.org/obo/NCIT_C70731 Sufficient SCDO:1000002 NCIT:C70731 Clinical Study Subject Unique Identifier Clinical Trial Subject Unique Identifier Clinical Trial Subject Unique Identifier NCIT:C70817 The formal plan of an experiment or research activity, including the objective, rationale, design, materials and methods for the conduct of the study; intervention description, and method of data analysis. Sufficient SCDO:1000096 NCIT:C70817 Study Protocol NCIT:C71375 A method of ultrasound imaging in which the ultrasound probe is pressed against the skin of the abdomen in order to create an image of the abdominal organs. Sufficient SCDO:0000005 NCIT:C71375 Abdominal Sonogram TUS Transabdominal Ultrasound Abdominal Ultrasound NCIT:C71746 Difficulties related to an apparatus used to gain access to arteries and veins. Sufficient SCDO:1000389 NCIT:C71746 Vascular Access Device Complications NCIT:C71754 Having no known name or identity or known source. Sufficient SCDO:0007242 NCIT:C71754 Anonymous NCIT:C74096 Of your own free will or design; not forced or compelled; controlled by individual volition. Sufficient SCDO:0001874 NCIT:C74096 Voluntary NCIT:C74954 The quantitative measurement of liver enzymes in the blood, which is useful in assessing the functional state of a patient's liver. Liver function tests include the measurement of albumin, alanine transaminase, aspartate transaminase, alkaline phosphatase, bilirubin, and gamma glutamyl transferase. Other LFTs to be added here? There are more in NCIT PhenX protocol: Liver Function - Assay #190801 Sufficient SCDO:0000695 NCIT:C74954 LFT Liver Function Assay Liver Function Assays Liver Function Tests Liver Function Test NCIT:C75434 Hemoglobin subunit alpha (142 aa, ~15 kDa) is encoded by both the human HBA1 and human HBA2 genes. This protein plays a role in the distribution of oxygen from the lungs to other organs and tissues. Sufficient SCDO:1000365 NCIT:C75434 Alpha Globin Alpha-Globin Alpha-Globin Chain Haemoglobin Alpha Chain Haemoglobin Subunit Alpha Hemoglobin Alpha Chain Hemoglobin Subunit Alpha Hemoglobin Subunit Alpha NCIT:C75583 Examination of the anterior segment of the eye using a medical instrument called a slit lamp. http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C75583 Sufficient SCDO:0001078 NCIT:C75583 SLIT LAMP Slit-Lamp Biomicroscopy Slit-Lamp Eye Exam Slit-Lamp Examination NCIT:C78254 Any problem arising from the use of a medical device. Sufficient SCDO:1000385 NCIT:C78254 Device Complication NCIT:C78393 Accumulation of iron in the tissues. It may be a manifestation of an inherited disorder (e.g., hemochromatosis) or acquired (in patients with repeated blood transfusions). Symptoms include hepatomegaly, arthritis, diabetes mellitus, and bronzed skin. If untreated it has a progressive course and may lead to death. Perhaps suggest that NCIT merges this term with "Hemochromatosis", which they have as a separate term. Sub-classes need to be worked on further. Consider sub-classes of "hemochromatosis" in the DO. Include Hemosiderosis as a sub-class? http://purl.obolibrary.org/obo/NCIT_C78393 Sufficient SCDO:0001945 NCIT:C78393 Diabetes Bronze Haemochromatosis Hemochromatosis Iron Storage Disorder Iron Overload NCIT:C78598 An acute or subacute reversible condition characterized by headaches, mental status changes, visual disturbances, and seizures associated with imaging findings of posterior leukoencephalopathy. It has been observed in association with hypertensive encephalopathy, eclampsia, and immunosuppressive and cytotoxic drug treatment. http://purl.obolibrary.org/obo/NCIT_C78598 Sufficient SCDO:0007836 NCIT:C78598 Reversible Posterior Leukoencephalopathy Syndrome Posterior Reversible Leukoencephalopathy NCIT:C78638 The development of a blood clot in a catheter. Sufficient SCDO:1000388 NCIT:C78638 Thrombus in Catheter NCIT:C78652 A parent report or patient self report for measuring health-related quality of life (HRQOL) in healthy children and adolescents and those with acute and chronic health conditions. The PedsQL Measurement Model uses a modular approach that integrates both generic core scales and disease-specific modules into one measurement system. (Copyright 1998-2008 James W. Varni, Ph.D.) Self; Proxy (Parent report) Clinic patients Many measures available in Spanish, French and Portuguese Toddlers; Children; Adolescents yes Sufficient SCDO:0000875 Varni, J. W., Seid, M., and Kurtin, P. S. (2001). PedsQL 4.0: Reliability and validity of the 86 pediatric quality of life inventory version 4.0 generic core scales in healthy and patient populations. Medical Care, 39, 800-812. NCIT:C78652 Pediatric Quality of Life Inventory PedsQL Pediatric Quality of Life Inventory (PedsQL) NCIT:C79903 A sample of blood applied in a thin film to a microscope slide for study under a microscope. Sufficient SCDO:0008915 NCIT:C79903 Blood Smear NCIT:C80411 A diagnostic procedure in which a catheter is guided into the right heart, where pressures may be measured and radiocontrast material may be injected to visualize blood flow in and around the right heart. http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C80411 Sufficient SCDO:0001012 NCIT:C80411 Pulmonary Artery Catheterization Swan-Ganz Catheterization Right Heart Catheterization NCIT:C81229 A description of an individual's current and past experience with alcoholic beverage consumption. Add other terms in the PhenX "Alcohol Use" collection? http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C81229 Sufficient SCDO:0000040 NCIT:C81229 Alcohol Use History NCIT:C81262 An identifying number within an institution that is used to reference a subject's medical information. Sufficient SCDO:1000853 NCIT:C81262 Medical Record Number NCIT:C82909 Anemia not associated with symptoms of fatigue, headaches, palpitations, or shortness of breath. In asymptomatic anemia the hematocrit levels usually range from 32 to 35%. http://purl.obolibrary.org/obo/NCIT_C82909 Sufficient SCDO:0003672 NCIT:C82909 Mild Anemia NCIT:C83031 The date on which a visit occurred. Sufficient SCDO:1000540 NCIT:C83031 Clinical Visit Date Visit Date NCIT:C84481 An inherited metabolic disorder characterized by iron accumulation in the tissues. Sufficient SCDO:0000512 NCIT:C84481 Congenital Haemochromatosis Hereditary Haemochromatosis Iron Overload Disease Primary Haemochromatosis Hereditary Hemochromatosis NCIT:C84979 Hemoglobin subunit epsilon (147 aa, ~16 kDa) is encoded by the human HBE1 gene. This protein plays a role in the transport of oxygen to tissues of the embryo. http://purl.obolibrary.org/obo/NCIT_C84979 Sufficient SCDO:0001381 NCIT:C84979 Epsilon-Globin Haemoglobin Epsilon Chain Haemoglobin Subunit Epsilon Hemoglobin Epsilon Chain Hemoglobin Subunit Epsilon NCIT:C84980 A type of polypeptide chain that when in combination with alpha globin polypeptide chains forms adult hemoglobin 2 (HbA2). HbA2 comprises around 3% of adult hemoglobin. Hemoglobin subunit delta (147 aa, ~16 kDa) is encoded by the human HBD gene. This protein plays a role in the transport of oxygen to tissues of the adult body. http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C84980 https://www.ncbi.nlm.nih.gov/gene/3045 Sufficient SCDO:1000011 NCIT:C84980 Delta Globin Delta-Globin Haemoglobin Delta Chain Haemoglobin Subunit Delta Hemoglobin Delta Chain Hemoglobin Subunit Delta NCIT:C84983 Hemoglobin subunit beta (147 aa, ~16 kDa) is encoded by the human HBB gene. This protein plays a role in the transport of oxygen to tissues of the adult body. Sufficient SCDO:1000358 NCIT:C84983 Beta Globin Beta Globin Chain Beta-Globin Beta-Globin Chain HBB Haemoglobin Beta Chain Haemoglobin Subunit Beta Hemoglobin Beta Chain Hemoglobin Subunit Beta NCIT:C85397 Measurement of the breathing capacity of the lung by means of a spirometer. Sufficient SCDO:0001100 NCIT:C85397 Spirometry NCIT:C86008 A product of hemoglobin produced by oxidation of the iron atom from the ferrous to the ferric state. Sufficient SCDO:1000167 NCIT:C86008 MetHb Methemoglobin NCIT:C91105 An instrument consisting of a predetermined set of questions for a clinical or research assessment. Sufficient SCDO:1000476 NCIT:C91105 Clinical or Research Assessment Questionnaire NCIT:C91106 A statement (either spoken or written) that is made in reply to a clinical research assessment question. Sufficient SCDO:1000473 NCIT:C91106 Clinical or Research Assessment Response Clinical or Research Assessment Answer NCIT:C92755 The biopsy of placental tissue containing the chorionic villi from the maternal uterus in early pregnancy to diagnose fetal genetic defects. http://purl.obolibrary.org/obo/NCIT_C92755 Sufficient SCDO:0000223 NCIT:C92755 CVS Chorionic Villus Sampling NCIT:C92803 Testing to determine if there is a predisposition or indication of a possible genetic or a chromosomal abnormality. http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C92803 Sufficient SCDO:0000446 NCIT:C92803 Genetic Screening NCIT:C92853 Hemorrhage defined as a blood loss in excess of 500 mL after vaginal delivery or more than 1000 mL after a cesarean delivery. Sufficient SCDO:0000916 NCIT:C92853 Postpartum Hemorrhage NCIT:C93407 Specific key measurement(s) or observation(s) used to measure the effect of experimental variables on the subjects in a study, or for observational studies, to describe patterns of diseases or traits or associations with exposures, risk factors or treatment. The specific measure that receives the most emphasis in assessment. http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C93407 Sufficient SCDO:0001116 NCIT:C93407 Study Outcome Measure Study Outcome Measurement NCIT:C95437 An acute inflammatory process that leads to necrosis of the pancreatic parenchyma. Signs and symptoms include severe abdominal pain, nausea, vomiting, diarrhea, fever, and shock. Causes include alcohol consumption, presence of gallstones, trauma, and drugs. http://purl.obolibrary.org/obo/NCIT_C95437 Sufficient SCDO:0005115 NCIT:C95437 Acute Pancreatitis NCIT:C95504 A form of alpha thalassemia that results from reduced protein production from three of the four alpha-globin genes. Clinically it is characterized by chronic hemolytic anemia. http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C95504 Sufficient SCDO:0000534 NCIT:C95504 Alpha-Thalassemia Intermedia Haemoglobin H Disease Hb H-Disease Hemoglobin H Disease NCIT:C95534 A condition in which a person is heterozygous for a globin gene, with one normal allele and one defective allele. NCIT includes this class below "Hemoglobinopathy", hence its inclusion here. http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C95534 Sufficient SCDO:0000550 NCIT:C95534 Heterozygous Hemoglobinopathy Hemoglobin Trait NCIT:C95535 A condition in which a person has reduced protein production from two of the four alpha-globin alleles. http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C95535 Sufficient SCDO:0000044 NCIT:C95535 Alpha-Thalassemia Trait -/- alpha/alpha or -/alpha -/alpha. It can exist in two forms: (1) alpha-thal-1 (alpha alpha/--), involves cis deletion of both alpha genes on the same chromosome; (2) alpha-thal-2 (alpha-/alpha-), involves trans deletion of alpha genes this occurs on different (homologous) chromosomes. Alpha Thalassemia Trait NCIT:C95536 A condition in which a person has reduced protein production from one of the four alpha-globin alleles. http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C95536 Sufficient SCDO:0000043 NCIT:C95536 Alpha Thalassemia Silent Alpha-Thalassemia Silent Carrier Alpha Thalassemia Silent Carrier NCIT:C95539 A compound heterozygous state in which a person has a hemoglobin S allele along with a beta-thalassemia allele. The severity of the condition is determined to a large extent by the quantity of normal hemoglobin produced by the beta-thalassemia gene. Sufficient SCDO:0001057 NCIT:C95539 Hb S-Beta Thalassemia HbS-Beta-Thalassemia Syndrome HbSBetaThal S Beta-Thalassemia S-Beta Thalassemia Sickle Beta Thalassaemia Sickle Beta-Thalassaemia Sickle Cell Beta Thalassemia Disease Sickle Cell Disease-S Beta Thalassaemia Sickle Cell-Beta Thalassaemia Sickle Cell-Beta-Thalassemia Sickle Cell-Beta-Thalassemia Disease Syndrome Sickle Beta Thalassemia NCIT:C96239 A morphologic finding indicating enlargement of the glomeruli in a kidney specimen. Sufficient SCDO:0002784 NCIT:C96239 Glomerular Hypertrophy NCIT:C96391 A conjugate vaccine of meningococcal polysaccharide used for active immunization against invasive meningococcal disease caused by Neisseria meningiditis serogroups A, C, Y, and W-135. http://purl.obolibrary.org/obo/NCIT_C96391 Sufficient SCDO:0006120 NCIT:C96391 MCV4 Menactra Meningococcal Conjugate Vaccine MCV-4 Meningococcal Polysaccharide (Serogroups A, C, Y and W-135) Diphtheria Toxoid Conjugated Vaccine Menveo Meningococcal Conjugate Vaccine MCV4 NCIT:C97120 An active immunizing vaccine used to prevent infection by the bacterium Streptococcus pneumoniae. It is indicated for disease caused by serotypes 1, 5, 4, 6B, 7, 9V, 14, 18C, 19F, and 23F. http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C97120 Sufficient SCDO:0000909 NCIT:C97120 PCV 10 Pneumococcal 10-Valent Conjugate Vaccine NCIT:C97121 A pneumococcal conjugate vaccine containing 13 different strains of the bacterium Streptococcus pneumoniae, used in children and studied in immunocompromised patients for the prevention of pneumococcal disease. The pneumococcal 13-valent conjugate vaccine contains capsular antigen polysaccharides derived from the S. pneumoniae serotypes 1, 3, 4, 5, 6A, 6B, 7F, 9V, 14, 18C, 19A, 19F and 23F that are individually conjugated to a nontoxic diphtheria cross-reactive material (CRM) carrier protein (CRM197). Upon vaccination, pneumococcal 13-valent conjugate vaccine induces active immunization against 13 different serotypes of S. pneumoniae and protects against pneumococcal disease. http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C97121 Sufficient SCDO:0000910 NCIT:C97121 PCV 13 PCV13 Vaccine Prevnar 13 Pneumococcal 13-Valent Conjugate Vaccine NCIT:C97123 An active immunizing vaccine used to prevent infection by the bacterium Streptococcus pneumoniae. It consists of a solution of saccharides of the capsular antigens of Streptococcus serotypes individually conjugated to proteins. http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C97123 Sufficient SCDO:0000275 NCIT:C97123 Pneumococcal Conjugate Vaccine Conjugate Pneumococcal Vaccine NCIT:C98805 Methemoglobinemia that is caused by exposure to certain drugs (xylocaine and benzene) and nitrate-rich foods. Sufficient SCDO:0000013 NCIT:C98805 Acquired Methemoglobinemia NCIT:C98835 A form of sickle cell thalassemia characterized by the absence of hemoglobin A. Patients usually have severe anemia identical to that seen in sickle cell disease. Requires further refinement. http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C98835 Sufficient SCDO:0001058 NCIT:C98835 Hb S Beta 0 Thalassemia Hemoglobin S Beta 0 Thalassemia S Beta 0 Thalassemia S beta-zero Sickle Beta 0 Thalassemia Sickle Beta Zero Thalassemia Sickle Cell-Beta 0 Thalassemia Sickle Cell-Beta Zero Thalassemia Sickle Cell Disease-S Beta Zero Thalassemia NCIT:C99042 The formation of a thrombus in the renal vein. http://purl.obolibrary.org/obo/NCIT_C99042 Sufficient SCDO:0005061 NCIT:C99042 Renal Vein Thrombosis NCIT:C99063 Ischemic necrosis of the spinal cord caused by occlusion of the arteries that supply blood to the spinal cord. Signs and symptoms include intermittent back pain, pain in the legs, paralysis, and incontinence. Can be treated with exchange transfusion (SCDO:0001303) http://purl.obolibrary.org/obo/NCIT_C99063 Sufficient SCDO:0005226 NCIT:C99063 Spinal Cord Infarction OBI:0000185 An assay that produces a picture of an entity. Perhaps replace this term with "Diagnostic Imaging" from NCIT? http://purl.obolibrary.org/obo/OBI_0000185 Sufficient SCDO:0000612 OBI:0000185 Imaging Assay OBI:0000626 A sequencing process which uses deoxyribonucleic acid as input and results in a the creation of DNA sequence information artifact using a DNA sequencer instrument. Add sub-class "beta-globin gene sequencing" as per the "Diagnostic Methods" section of the term "Dominant beta-thalassemia" in Orphanet. Sufficient SCDO:0004249 OBI:0000626 DNA Sequencing OBI:0000925 A material entity bearing the disposition to infect an organism Sufficient SCDO:0000638 OBI:0000925 Infectious Agent OBI:0000990 A microscope that produces an image of an object by targeting it with an electron beam. Sufficient SCDO:0000422 OBI:0000990 It is capable of much higher magnifications and has a greater resolving power than a light microscope, allowing it to see much smaller objects in finer detail. Electron Microscope OBI:0001098 A device that is used to visualize subcutaneous body structures including tendons, muscles, joints, vessels and internal organs. Sufficient SCDO:0001202 OBI:0001098 Ultrasound Machine OBI:0001138 A device that is used to generate X-rays. http://purl.obolibrary.org/obo/OBI_0001138 Sufficient SCDO:0001251 OBI:0001138 Radiographic Unit X-Ray Machine OBI:0002140 An assay to determine the temperature of an evaluant. Sufficient SCDO:1000752 OBI:0002140 Temperature Measurement Assay OBI:0002146 An antigen specific antibodies assay that is meant to detect antibodies that bind to human immunodeficiency virus (HIV) antigens. Sufficient SCDO:1000195 OBI:0002146 HIV Antibody Assay The window period for antibody tests in most people is somewhere between 3 to 12 weeks from the time of infection. HIV Antibody Test OBI:0002556 A value specifcation that specifies the youngest age when specifying an age range. Sufficient SCDO:1000405 OBI:0002556 Minimum Age Value Specification OBI:0002557 A value specifcation that specifies the oldest age when specifying an age range. Sufficient SCDO:1000404 OBI:0002557 Maximum Age Value Specification OBI:0200198 A data transformation that uses two or more analyzers separated by a region in which ions can be induced to fragment by transfer of energy (frequently by collision with other molecules). Sufficient SCDO:0001138 OBI:0200198 MS/MS Tandem MS Example of usage: A precursor ion is selected in the first stage, allowed to fragment and then all resultant masses are scanned in the second mass analyzer and detected in the detector that is positioned after the second mass analyzer. This experiment is commonly performed to identify transitions used for quantification by tandem MS. Tandem Mass Spectrometry OBI:0400115 A spectrophotometer is an instrument that measures the intensity of light as a function of the color, or more specifically, the wavelength of light, transmitted by a substance. Sufficient SCDO:0001096 OBI:0400115 Spectrophotometer OBI:0400169 A microscope is an instrument which magnifies the view on objects (too small to be viewed by the naked eye) under increased resolution. A microscope can be an optical instrument but also and electronic instrument. There are various kind of optical microscopes, e.g confocal microscope, epifluoresence microscope). Sufficient SCDO:0000757 OBI:0400169 Microscope OBI:1110053 A disease characterized by abnormal and uncontrolled cell division. http://purl.obolibrary.org/obo/OBI_1110053 Sufficient SCDO:0000180 OBI:1110053 Malignancy Malignant Neoplasia Malignant Neoplasm Malignant Tumor Malignant Tumour Cancer OGMS:0000023 A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species. Sub-classes to be added?: -- increased lactate dehydrogenase level (in Ontology of Adverse Events AOE) -- decreased lactate dehydrogenase level (Mammalian Phenotype Ontology) -- Splenomegaly (link this to Spleen Examination) -- Obstructive Hydrocephalus (see "Cerebellar Hemorrhage") -- Failure to Thrive (MeSH) -- Cardiac Output, Low (MeSH) -- Cardiac Output, High (MeSH) -- Add the sub-class "Clinical Phenotype" from Ontology for General Medical Science http://bioportal.bioontology.org/ontologies/OGMS?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOGMS_0000023 Sufficient SCDO:0000893 OGMS:0000023 Phenotype OGMS:0000028 A clinically abnormal phenotype that is characteristic of a single disease. Sufficient SCDO:1000185 OGMS:0000028 Disease Phenotype OGMS:0000046 A disorder whose etiology involves (1) a modification to the patient's genomic DNA which leads to alterations in the normal expression pattern of the genome, but is (2) not a change in the nucleotide sequence. http://purl.obolibrary.org/obo/OGMS_0000046 Sufficient SCDO:0000439 OGMS:0000046 Epigenomic Disorder Epigenetic Disorder OGMS:0000047 A disorder whose etiology involves an abnormality in the nucleotide sequence of an organism's genome. http://purl.obolibrary.org/obo/OGMS_0000047 Sufficient SCDO:0000445 OGMS:0000047 Genetic Disorder OGMS:0000051 A genetic disorder inherited during conception that is part of all cells in the organism. Perhaps remove this class but keep sub-classes? Or include the class "Acquired Genetic Disorder" as a sibling of this class if terms are included that can be sub-classes of it? http://purl.obolibrary.org/obo/OGMS_0000051 Sufficient SCDO:0000279 OGMS:0000051 Constitutional Genetic Disorder OGMS:0000088 A communication from a patient about something they perceive as being abnormal about their body or life. http://purl.obolibrary.org/obo/OGMS_0000088 Sufficient SCDO:0000872 OGMS:0000088 Patient Symptom Report OPMI:0000023 An answer to question where the answer is Yes. Sufficient SCDO:1000563 OPMI:0000023 yes answer to question Yes OPMI:0000024 An answer to question where the answer is No. Sufficient SCDO:1000564 OPMI:0000024 no answer to question No OPMI:0000025 An answer to question that indicates the response to the specified question is unknown. Sufficient SCDO:1000562 OPMI:0000025 Don't know unknown answer to question Do Not Know OPMI:0000027 An answer to question where one declines to answer the specified question. Sufficient SCDO:1000561 OPMI:0000027 Refuse to answer Refused to answer declined to answer question declined to answer to question Refused OPMI:0000028 An answer to question that is not enumerated in the list and then may be entered with free text in a separate text box Sufficient SCDO:1000565 OPMI:0000028 other answer to question Other PR:000001318 A protein that is a translation product of the human SELL gene or a 1:1 ortholog thereof. It is a leukocyte adhesion receptor that play an important role in regulating the inflammatory response by mediating leukocyte tethering and rolling on adherent leukocytes. Sufficient SCDO:1000443 PR:000001318 CD62 Antigen-Like Family Member L CD62L Lymph Node Homing Receptor L-selection is a serum marker for neutrophil activation. L-Selectin SBO:0000316 Single-stranded RNA molecules thought to regulate the expression of other genes. miRNAs are encoded by genes that are transcribed from DNA but not translated into protein (non-coding RNA). Sufficient SCDO:0000756 SBO:0000316 miRNA MicroRNA SCDO:0000006 The performance of the basic activities of self care, such as dressing, ambulation, or eating. http://purl.bioontology.org/ontology/MESH/D000203 Sufficient SCDO:0000006 MESH:D000203 ADL Daily Living Activities Daily Living Activity Self Care (Rehabilitation) Self-Care Ability to Carry Out Activities of Daily Living SCDO:0000007 A structurally abnormal hemoglobin that occurs in one or more forms of Sickle Cell Disease (SCD). Probably too specific to SCD be included in other ontologies. None SCDO (Jade Hotchkiss) Structurally Abnormal Hemoglobin Present in SCD Abnormal Hemoglobin in SCD SCDO:0000008 Abnormality in structure and function of the Red Blood Cell. Are there other relevant erythrocyte abnormalities that can be included as children here? If not, this class can be removed and just keep "Abnormal Hemoglobin". http://purl.obolibrary.org/obo/HP_0001877 Sufficient Abnormality of Red Blood Cell Abnormality of Red Blood Cells deprecated Abnormality of Erythrocytes true SCDO:0000010 Analgesic antipyretic derivative of acetanilide. It has weak anti-inflammatory properties and is used as a common analgesic, but may cause liver, blood cell, and kidney damage. Sufficient SCDO:0000010 MESH:D000082 Paracetamol Tylenol Acetaminophen SCDO:0000016 A condition that co-exists or follows from sickle cell disease and that has a severe and rapid onset of symptoms with short duration. Probably too specific to warrant inclusion into anther ontology. None SCDO http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C14140 http://purl.bioontology.org/ontology/MESH/Q000150 Acute Complications of SCD Acute Complications of Sickle Cell Disease SCDO:0000018 An acute onset of wheezing in a person with SCD who has no co-morbid asthma. Check and show which source was used for the description and whether the description was adapted from the source. -- Provide source for additional info. Cohen et al 2011 Am J Hematol., Glassberg et al 2014 Curr Opin Pediatr., Knight-Madden et al 2014 Ped Resp Rev Etiology may be unclear. May be related to inflammation of SCD and/or viral lower respiratory tract infection. Normal Chest X-ray None Cohen et al 2011 Am J Hematol., Glassberg et al 2014 Curr Opin Pediatr., Knight-Madden et al 2014 Ped Resp Rev Too specific to SCD to be included in other ontologies? PFTs may be done to asses for airway hyper-responsiveness. Acute Non-Specific Wheezing Episode SCDO:0000019 Sickle cell pain management that aims to heal the acute process. Request inclusion into MESH below "Pain Management" / "Sickle Cell Pain Management" (also to be suggested for inclusion) None SCDO Acute Sickle Cell Pain Treatment Acute Sickle Cell Pain Management SCDO:0000021 An acute respiratory illness with no lower respiratory tract signs or infiiltrate on chest radiograph. Request inclusion into relevant ontology Few but definitions not freely available SCDO Acute Upper Respiratory Infection URI URTI Acute Upper Respiratory Tract Infection SCDO:0000024 The extent to which a person's behaviour - taking medications, following a diet and/or executing life style changes, corresponds to agreed recommendations by a health care provider. Suggest update to description for "Patient Compliance" in MESH. Suggest update to description MESH:D010349 Adherence to Long Term Therapy Patient Adherence Patient Compliance Patient Cooperation deprecated-Adherence true SCDO:0000026 A 20-item questionnaire that assesses the frequency of severe headaches, the level of pain, whether the person is taking medications, and associated complications such as nausea. Suggest update to label in PhenX (from "Migraine - Adult") as we have done. PhenX protocol: Migraine - Adult #130501 Suggest update to label phenX:130501 Adult Migraine Questionnaire SCDO:0000028 An adverse event that occurs after a drug administration. Should this be a sub-class of "Environmental Disease Modifier"? http://purl.obolibrary.org/obo/OAE_0000005 Sufficient SCDO:0000028 OAE:0000005 ADE ADR Adverse Drug Reaction Drug Adverse Event Adverse Drug Event SCDO:0000029 Electrophoresis in which agar or agarose gel is used as the diffusion medium. http://purl.bioontology.org/ontology/MESH/D004587 Sufficient SCDO:0000029 MESH:D004587 Agar Gel Electrophoresis Agarose Gel Electrophoresis SCDO:0000032 A rare congenital disorder characterized by a partial or complete absence (agenesis) of an area of the brain that connects the two cerebral hemispheres. It can be the result of a failure in any one of the multiple steps of callosal development including cellular proliferation and migration, axonal growth or glial patterning at the midline. Suggest update to description in HPO. Include links to relevant Therapeutics. http://rarediseases.org/rare-diseases/agenesis-of-corpus-callosum/ Suggest update to description ACC Absence of Corpus Callosum Absent Corpus Callosum Agenesis of the Corpus Callosum Callosal Agenesis Corpus Callosum Agenesis Dysplastic or Absent Corpus Callosum Agenesis of Corpus Callosum SCDO:0000034 A quantitative measurement of alanine aminotransferase present in a blood sample. Suggest update to description in NCIT (from "Alanine Aminotransferase Measurement") Suggest update to description NCIT:C64433 ALT Blood Test Alanine Transaminase Blood Test Circulating Alanine Transaminase Test SGPT Test Serum Glutamic-Pyruvic Transaminase Test Alanine Aminotransferase Blood Test SCDO:0000035 The amount of alanine aminotransferase present in a specified volume of blood. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) ALT Level Alanine Aminotransferase Level Alanine Transaminase Level Blood Alanine Transaminase Level Circulating Alanine Transaminase Level SGPT Level Serum Glutamic-Pyruvic Transaminase Level Alanine Aminotransferase Level SCDO:0000037 Increased concentration of albumin in the urine; more than 30mg in 24hours or urine albumin creatinine ratio (ACR) >3 mg/mmol. Suggest update to description in HPO. http://www.nice.org.uk/guidance/CG182/chapter/introduction Suggest update to description in HPO. HP:0012592 Because albuminuria may be affected by non-pathological factors (exercise, menstruation contamination, biological variability, etc.), abnormal values should be confirmed within 1-2 months. Albuminuria SCDO:0000038 An indication of whether the respondent has ever consumed any alcoholic beverage during his or her entire life. Request inclusion into relevant ontology Not relevant to context of sickle cell SCDO (Jade Hotchkiss) Alcohol - Lifetime Use SCDO:0000042 A disorder characterized by reduced synthesis of the alpha chains of hemoglobin. The severity of this condition can vary from mild anemia to death, depending on the number of genes deleted. A hemoglobinopathy with two clinically significant forms: hemoglobin Bart hydrops fetalis (deletion of all 4 alpha-globin genes; --/--) which is severe and often results in neonatal death; and hemoglobin H disease (most commonly caused by deletion of 3 alpha-globin genes; --/-alpha) which results in hemolytic anemia, splenomegaly and bone changes. Curation completed by the SCDO curator team: Clair. Origa R, Moi P. Alpha-Thalassemia. 2005 Nov 1 [Updated 2016 Dec 29]. In: Adam MP, Ardinger HH, Pagon RA, et al., editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle 1993-2018. Available from: https://www.ncbi.nlm.nih.gov/books/NBK1435/ http://purl.bioontology.org/ontology/MESH/D017085 Sufficient SCDO:0000042 MESH:D017085 A-Thalassemia Alpha-Thalassemia Thalassemia Alpha Alpha Thalassemia SCDO:0000045 Drugs that selectively bind to and activate alpha adrenergic receptors. http://purl.bioontology.org/ontology/MESH/D000316 Sufficient SCDO:0000045 MESH:D000316 Adrenergic Alpha Agonists Adrenergic Alpha-Agonists Alpha Adrenergic Receptor Agonist Alpha-Adrenergic Agents SCDO:0000046 A region of chromosome 16 that includes five functional genes and two pseudogenes. The order of genes is: 5' - zeta - pseudozeta - mu - pseudoalpha-1 - alpha-2 -alpha-1 - theta1 - 3'. It is responsible for the creation of the alpha parts (roughly half) of the oxygen transport protein Hemoglobin. Request inclusion into relevant ontology perhaps below "Genetic Locus"/"Globin Locus" (also to be included) in MESH. None SCDO (Jade Hotchkiss) Alpha-Globin Gene Cluster Alpha-Globin Locus SCDO:0000049 Methods of pain relief that may be used with or in place of analgesics. http://purl.bioontology.org/ontology/MESH/D000698 Sufficient SCDO:0000049 MESH:D000698 Analgesias Analgesia SCDO:0000050 A compound capable of relieving pain without the loss of consciousness. http://purl.bioontology.org/ontology/MESH/D000700 Sufficient SCDO:0000050 MESH:D000700 Analgesic Analgesic Agent Analgesic Drugs Anodynes Antinociceptive Agent Pain Killers Painkiller Painkillers Analgesic SCDO:0000053 An adverse drug event that results in unexpected and unwanted events due to anesthetic drug treatment. http://purl.obolibrary.org/obo/OAE_0002348 Sufficient SCDO:0000053 OAE:0002348 Anesthetic Complication AE SCDO:0000054 Grayish, brown, or dark red streaks caused by cracks in Bruch's membrane that are histologically characterized by calcium deposition. Angioid streaks are most characteristic of sickle cell anemia and can occur to a lesser extent in other sickle cell syndromes, but not in sickle cell trait. Suggest update to description in DO. Currently no description. Ballas et al 2010 Am J Hematol Suggest update to description DOID:13401 Angioid Streaks SCDO:0000055 A class of drugs whose main indications are the treatment of hypertension and heart failure. They exert their hemodynamic effect mainly by inhibiting the renin-angiotensin system. They also modulate sympathetic nervous system activity and increase prostaglandin synthesis. They cause mainly vasodilation and mild natriuresis without affecting heart rate and contractility. http://purl.bioontology.org/ontology/MESH/D000806 Sufficient SCDO:0000055 MESH:D000806 ACE ACE Inhibitors Angiotensin Converting Enzyme Angiotensin Converting Enzyme Inhibitors Angiotensin-Converting Enzyme Inhibitors SCDO:0000056 The respondent's total family income from the last calendar year. Request inclusion into MESH below "Income". The PhenX protocol is U.S. specific. Is there one relevant to the African setting? PhenX protocol: Annual Family Income #11101 Negligable phenX:11100 Annual Family Income SCDO:0000057 Substance that reduces or suppresses inflammation. http://purl.bioontology.org/ontology/MESH/D000893 Sufficient SCDO:0000057 MESH:D000893 Anti Inflammatories Anti Inflammatory Agents Anti-Inflammatories Anti-Inflammatory Agents Anti-Inflammatory Drug Antiinflammatories Antiinflammatory Agents Anti-Inflammatory Agent SCDO:0000066 Drugs that bind to but do not activate histamine receptors, thereby blocking the actions of histamine or histamine agonists. Classical antihistaminics block the histamine H1 receptors only. http://purl.bioontology.org/ontology/MESH/D006633 Sufficient SCDO:0000066 MESH:D006633 Antihistamines Histamine Antagonist Histamine Antagonists Antihistamine SCDO:0000067 Used in the treatment of acute or chronic vascular hypertension regardless of pharmacological mechanism. Among the antihypertensive agents are diuretics; (especially diuretics, thiazide); adrenergic aeta-antagonists; adrenergic alpha-antagonistics; angiotensin-converting enzyme inhibitors; calcium channel blockers; ganglionic blockers; and vasodilator agents. http://purl.bioontology.org/ontology/MESH/D000959 Sufficient SCDO:0000067 MESH:D000959 Agents, Antihypertensive Anti Hypertensive Agent Anti-Hypertensives Antihypertensive Drug Antihypertensive Drugs Antihypertensives Antihypertensive Agents SCDO:0000069 This gene encodes a secreted high density lipoprotein which binds to apolipoprotein A-I. Variants in the APOL1 gene can influence susceptibility to end-stage renal disease and Trypanosomiasis (African Sleeping Sickness). Exists in other ontologies but we have provided a description more relevant to its relationship with SCD. http://www.ncbi.nlm.nih.gov/gene/8542 Not relevant to context of sickle cell APO-L APOL APOL1 Gene Apolipoprotein L1 Gene APOL1 SCDO:0000070 Exercises performed in or underwater for conditioning or rehabilitation (e.g., in injured athletes or patients with joint diseases). Request inclusion into relevant ontology http://medical-dictionary.thefreedictionary.com/aquatic+therapy None Aqua Therapy Hydrotherapy Aquatic Rehabilitation SCDO:0000071 A hematology assay that measures the acidity (pH) and the levels of oxygen and carbon dioxide in the blood from an artery. This test is used to check how well the lungs are able to move oxygen into the blood and remove carbon dioxide from the blood. Sufficient SCDO:0000071 ERO:0000533 ABG Test Arterial Blood Gas Test SCDO:0000072 Abnormal formation of blood vessels that shunt arterial blood directly into veins without passing through the CAPILLARIES. They usually are crooked, dilated, and with thick vessel walls. A common type is the congenital arteriovenous fistula. The lack of blood flow and oxygen in the capillaries can lead to tissue damage in the affected areas. http://purl.bioontology.org/ontology/MESH/D001165 Sufficient SCDO:0000072 MESH:D001165 Arteriovenous Malformations Arteriovenous Malformation SCDO:0000073 A water-soluble, semi-synthetic derivative of the sesquiterpene lactone artemisinin with anti-malarial, anti-schistosomiasis, antiviral, and potential anti-neoplastic activities. Sufficient SCDO:0000073 MESH:D000077332 Artesunic Acid Dihydroartemisinine 12 Alpha Succinate Artesunate SCDO:0000078 The score obtained from the Adult Sickle Cell Quality-of-Life Measurement Information System (ASCQ-Me). Is this term acceptable? If so, request inclusion into relevant ontology None SCDO (Jade Hotchkiss) http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820201 ASCQ-Me - Quality of Life in SCD Sickle Cell Disease Adult Quality of Life Questionnaire Assessment Score deprecated ASCQ-Me Score true SCDO:0000079 A bioassay to measure levels of aspartate aminotransferase (AST), which is released into the blood following tissue damage. Suggest update to PhenX label ("Aspartate Aminotransferase Level") also to NCIT label (from "Aspartate Aminotransferase Measurement") Suggest update to label phenX:811201 AST Blood Test Aspartate Transaminase Blood Test Serum AST Blood Test Aspartate Aminotransferase Blood Test SCDO:0000080 The amount of aspartate aminotransferase present in a specified volume of blood. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) AST Level Aspartate Transaminase Level Blood Aspartate Transaminase Amount Aspartate Aminotransferase Level SCDO:0000081 A set of 27 questions administered to adults with sickle cell disease (SCD) to determine the quality of care that they have received from health care providers. Suggest update to label in PhenX (from "Quality of Care") http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820101 PhenX protocol: Quality of Care - Adults #820101 Self Clinic Patients (Adults with SCD) These questions are used to assess the patient-reported health care needs and quality of service from health care providers for individuals with chronic conditions such as sickle cell disease (SCD). 18 and older Suggest update to label SCDO Keller, S. D., Yang, M., Treadwell, M. J., Werner, E. M., & Hassell, K. L. (2014). Patient reports of health outcome for adults living with sickle cell disease: Development and testing of the ASCQ-Me item banks. Health and Quality of Life Outcomes, 12(1), 125. doi:10.1186/s12955-014-0125-0 ASCQ-Me Quality of Care Module ASCQ-Me - Quality of Care in SCD SCDO:0000082 A planned process with the objective of producing diagnostic information about the material entity that is the evaluant, by physically examining it or its proxies. Possibly too specifiic to this ontology to be included in another ontology? Use structuring of sub-classes within MESH's "Diagnostic Techniques and Procedures" and NCIT's "Diagnostic Procedure" to inform structuring of terms in this class. None SCDO (Jade Hotchkiss) http://purl.obolibrary.org/obo/OBI_0000070 Diagnostic Assay Diagnostic Method Diagnostic Technique Diagnostic Test Diagnostic Technique, Method, Test or Assay SCDO:0000084 This measure is a magnetic resonance imaging (MRI) method of capturing an individual's heart performance, and is considered the gold standard for capturing ventricular volumes and mass. It is used to detect cardiac abnormalities, such as cardiomyopathies, myocardial fibrosis, and infarction. Request inclusion into relevant ontology. Perhaps in the CPT. http://www.phenxtoolkit.org/toolkit_content/supplemental_info/scd_cardio_pulm_renal/measures/Short_Axis_Function_20May2015.doc None MRI of Short-Axis Cardiac Function Assessment of Short-Axis Cardiac Function by MRI SCDO:0000086 A form of bronchial disorder with three distinct components: airway hyper-responsiveness, airway inflammation, and intermittent airway obstruction. It is characterized by spasmodic contraction of airway smooth muscle, wheezing and dyspnea. Further work: is caused by links to be moved to object property links Include a copy of this term below "Comorbid Disease" and/or below "Respiratory System". http://purl.bioontology.org/ontology/MESH/D001249 Airway hyper-responsiveness Airway inflammation Intermittent airway obstruction It is characterized by spasmodic contraction of airway smooth muscle, wheezing and dyspnea. Sufficient SCDO:0000086 MESH:D001249 Asthma SCDO:0000088 A chronic inflammatory genetically determined disease of the skin marked by increased ability to form reagin (IgE), with increased susceptibility to allergic rhinitis and asthma, and hereditary disposition to a lowered threshold for pruritus. It is manifested by lichenification, excoriation, and crusting, mainly on the flexural surfaces of the elbow and knee. In infants it is known as infantile eczema. Sufficient SCDO:0000088 MESH:D003876 Atopic Eczema Baby Eczema Infantile Eczema Atopic Dermatitis SCDO:0000094 This gene encodes a C2H2 type zinc-finger protein by its similarity to the mouse Bcl11a/Evi9 protein. During hematopoietic cell differentiation, this gene is down-regulated. It is possibly involved in lymphoma pathogenesis since translocations associated with B-cell malignancies also deregulates its expression. Multiple transcript variants encoding several different isoforms have been found for this gene. Link to "Hereditary Persistence of fetal hemoglobin". Request inclusion into relevant ontology http://www.ncbi.nlm.nih.gov/gene/53335 Not relevant to context of sickle cell B-Cell CLL/Lymphoma 11A Gene B-cell CLL/lymphoma 11A (zinc finger protein) B-cell CLL/lymphoma 11A Gene BAF Chromatin Remodeling Complex Subunit BCL11A Gene BCL-11A Gene BCL11A Gene Fetal Hemoglobin Quantitative Trait Locus 5 HBFQTL5 BCL11A SCDO:0000098 One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal. Bacteria can be classified by their response to oxygen: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophy (via chemical reaction) or phototrophy (via light reaction); for chemotrophs by their source of chemical energy: chemolithotrophy (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for carbon; nitrogen; etc.; heterotrophy (from organic sources) or autotrophy (from carbon dioxide). They can also be classified by whether or not they stain (based on the structure of their cell walls) with crystal violet dye: gram-negative or gram-positive. http://purl.bioontology.org/ontology/MESH/D001419 Sufficient SCDO:0000098 MESH:D001419 Bacteria SCDO:0000102 The BAI is the most widely used instument for measuring anxiety. It consists of 21 items to assess how bothersome a symptom of anxiety has been for the subject over the past month. Scoring the BAI is based on a 0-3 point scale with higher scores indicating severity. Request inclusion into relevant ontology. Could be as a child of "Symptom Specific Assessment Tool" in the NCIT. Beck, A. T., Epstein, N., Brown, G., & Steer, R. A. (1988). An inventory for measuring clinical anxiety: psychometric properties. Journal of Consulting and Clinical Psychology, 56, 893-897. Multiple countries and cultural groups Self Clinic Patients Spanish 17 years and older yes Few but definitions not freely available BAI Beck Anxiety Inventory Beck Anxiety Inventory (BAI) SCDO:0000104 The Behavior Rating Inventory of Executive Function (BRIEF) is a detailed questionnaire designed to assess executive function behaviors of children and adolescents in the school and home environments. The BRIEF is completed by parents and teachers. Suggest update to label in PhenX. PhenX protocol: #131102 Suggest update to label phenX:131102 BRIEF Executive Function - Child Behavior Rating Inventory of Executive Function SCDO:0000106 The actions or reactions of a person in response to a situation or stimuli. Few but definitions not specific enough SCDO Behaviour SCDO:0000107 Personal or collective understanding of what the causes (could be predisposing factors, enabling factors, precipitating factors, reinforcing factors, and/or risk factors) are of a certain illness. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) http://purl.bioontology.org/ontology/MESH/D015984 Beliefs about Causality Cultural beliefs, such as re-incarnation and witchcraft, may influence notions on causality of sickle cell disease. Beliefs About Causes of Illness SCDO:0000108 Personal or collective understanding of what can remedy or treat illness. Request inclusion into relevant ontology, perhaps MESH. none SCDO http://www.ncbi.nlm.nih.gov/mesh/68003469 Beliefs About Remedies and Treatment SCDO:0000110 A beta-thalassemia caused by the reduced (beta-) synthesis of the beta globin chains of the hemoglobin (Hb) tetramer. Request inclusion into relevant ontology, perhaps DOID. A. Cao and R. Galanello, "Beta Thalassemia", Genetics in Medicine, Vol. 12, No. 2, 2010, pp. 61 76. doi:10.1097/GIM.0b013e3181cd68ed None Beta - Thalassemia Beta Minus-Thalassemia Beta- Thalassemia Beta-Minus-Thalassemia Beta Minus Thalassemia SCDO:0000111 A hemoglobinopathy characterized by the reduced (beta plus) or absent (beta zero) synthesis of the beta globin chains of hemoglobin, resulting in variable outcomes ranging from severe anemia to clinically asymptomatic individuals. Suggest update to description in DOID. Include a "Dominant Beta-Thalassemia" sub-class? (see Orphanet) A. Cao and R. Galanello, "Beta Thalassemia", Genetics in Medicine, Vol. 12, No. 2, 2010, pp. 61 76. doi:10.1097/GIM.0b013e3181cd68ed Origa R. Beta-Thalassemia. 2000 Sep 28 [Updated 2018 Jan 25]. In: Adam MP, Ardinger HH, Pagon RA, et al., editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle 1993-2018. Available from: https://www.ncbi.nlm.nih.gov/books/NBK1426/ http://en.wikipedia.org/wiki/Beta_thalassemia http://purl.obolibrary.org/obo/DOID_12241 Suggest update to description DOID:12241 Beta Thalassemias Beta Type Thalassemia Beta-Thalassemia Beta-Thalassemias Hemoglobin F Disease Mediterranean Anemia Beta Thalassemia SCDO:0000112 A homozygous (B+/B+) or compound heterozygous (B0/B+) form of beta-thalassemia characterized by mild to moderate anemia which does not or only occasionally requires transfusion. Sufficient SCDO:0000112 ORPHA:231222 B+/B+ B0/B+ Beta-Thalassemia Intermedia Thalassemia Intermedia Beta Thalassemia Intermedia SCDO:0000113 A severe early-onset form of beta thalassemia characterized by severe anemia requiring regular red blood cell transfusions. Sufficient SCDO:0000113 ORPHA:231214 B0/B0 BT Major Beta-Thalassemia Major Cooley Anemia Cooley's Anemia Mediterranean Anemia Thalassemia Major Beta Thalassemia Major SCDO:0000114 The inheritance of only one mutated beta-globin allele (beta+ or beta0). Request inclusion into relevant ontology. Perhaps below "clinical subtype" in Orphanet. The exact synonym "B+/B" has been changed to "B-/B", as per the change in convention from "Beta Plus Thalassemia" to "Beta Minus Thalassemia". http://en.wikipedia.org/wiki/Beta_thalassemia Few but definitions not freely available B-/B B0/B Beta Thalassemia Minor Beta-Thalassemia Trait Heterozygosity for Beta-Thalassemia Heterozygous Beta-Thalassemia Beta Thalassemia Trait SCDO:0000115 Beta-zero thalassemia is a form of beta-thalassemia in which beta-globin chain synthesis is absent. The clinical phenotype is often that of transfusion-dependant beta thalassemia major, however modifying factors may ameliorate the symptoms of severe anemia (Cao & Gallanelo, 2010). Request inclusion into relevant ontology, perhaps DOID. A. Cao and R. Galanello, "Beta Thalassemia", Genetics in Medicine, Vol. 12, No. 2, 2010, pp. 61 76. doi:10.1097/GIM.0b013e3181cd68ed None Beta 0 Thalassemia Beta Zero-Thalassemia Beta-Zero-Thalassemia Beta0 Thalassemia Hb Beta Zero-Thalassemia Hb F only Beta Zero Thalassemia SCDO:0000116 A globin locus composed of five genes located on a short 45 kb region of chromosome 11. The order of genes in this cluster is: 5' - epsilon - gamma-G - gamma-A - delta - beta - 3'. It is responsible for the creation of the beta parts (roughly half) of the oxygen transport protein Hemoglobin. Request inclusion into relevant ontology perhaps below "Genetic Locus"/"Globin Locus" (also to be included) in MESH. None SCDO (Jade Hotchkiss) Beta-Globin Cluster Beta-Globin Gene Cluster HBB Locus Beta-Globin Locus SCDO:0000117 Defined arrays of polymorphic gene sites that are inherited together across the genetic vicinity of the beta-globin gene or gene cluster on chromosome 11. Request inclusion into relevant ontology Nagel, et. al. NEngl J Med. 1985 Apr 4;312(14):880-4 None SCDO Beta-Globin Haplotypes Beta-Haplotypes Beta-S Haplotype Beta-S Haplotypes Beta-Globin Haplotype SCDO:0000119 A bioassay to measure levels of bilirubin, a yellow substance found in bile produced when the liver breaks down old red blood cells. Suggest update to label in PhenX (from "Bilirubin Level"). Suggest update to label phenX:810901 Bilirubin Blood Test SCDO:0000120 An analytical in vitro procedure used to detect, quantify and/or study the binding or activity of a biological molecule, such as an enzyme. Request inclusion into relevant ontology. http://www.nature.com/subjects/biochemical-assays Negligable Biochemical Assay SCDO:0000122 A biological factor that modifies one or more aspects of a disease, such as sickle cell disease (SCD) (e.g. aspects such as temporal pattern, age of onset and mortality), for specific phenotype(s) of the disease. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) Biological Disease Modifier SCDO:0000123 The country in which the respondent was born. Request inclusion into relevant ontology http://www.phenxtoolkit.org/index.php?pageLink=browse.protocols&id=010200 Negligable Place of Birth Birthplace SCDO:0000124 The country in which the respondent's biological father was born. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) Birthplace of Biological Father SCDO:0000125 The country in which the respondent's biological mother was born. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) Birthplace of Biological Mother SCDO:0000126 The country or countires in which the respondent's biological grandparents were born. Request inclusion into relevant ontology There is a protocol in PhenX but it is US specific. Negligable SCDO (Jade Hotchkiss) Birthplace of Grandparents SCDO:0000127 The country in which the respondent's biological maternal (on the mother's side of the family) grandfather was born. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) Birthplace of Maternal Grandfather SCDO:0000128 The country in which the respondent's biological maternal (on the mother's side of the family) grandmother was born. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) Birthplace of Maternal Grandmother SCDO:0000129 The country or countires in which the respondent's biological parents were born. Request inclusion into relevant ontology There is a protocol in PhenX but it is US specific. Negligable SCDO (Jade Hotchkiss) Birthplace of Parents SCDO:0000130 The country in which the respondent's biological paternal (on the father's side of the family) grandfather was born. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) Birthplace of Paternal Grandfather SCDO:0000131 The country in which the respondent's biological paternal (on the father's side of the family) grandmother was born. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) Birthplace of Paternal Grandmother SCDO:0000132 Black lesions in the retina that form at the border of perfused and nonperfused retina that are caused by the migration of hyperplastic retinal pigment epithelial cells into sensory retina. The sensory retina surrounding the lesion is atrophic. Request inclusion into relevant ontology. Ballas et al 2010 Am J Hematol None Black Sunburst Lesion SCDO:0000133 Test used in the analysis of the hemic system. http://purl.bioontology.org/ontology/MESH/D006403 Sufficient SCDO:0000133 MESH:D006403 Blood Assay Blood Tests Hematologic Test Hematologic Tests Hematological Test HematologyTest Blood Test SCDO:0000138 The transfer of blood components such as erythrocytes, leukocytes, platelets, and plasma from a donor to a recipient or back to the donor. This process differs from the procedures undertaken in plasmapheresis and types of cytapheresis; (plateletpheresis and leukapheresis) where, following the removal of plasma or the specific cell components, the remainder is transfused back to the donor. http://purl.bioontology.org/ontology/MESH/D016913 Sufficient SCDO:0000138 MESH:D016913 Blood Component Transfusion SCDO:0000139 Test to determine the presence of blood infection (e.g. sepsis; bacteremia). Sufficient SCDO:0000139 MESH:D000071997 BC Culture Blood Haemoculture Hemoculture Blood Culture SCDO:0000147 The introduction of whole blood or blood component directly into the blood stream. (Dorland, 27th ed) http://purl.bioontology.org/ontology/MESH/D001803 Sufficient SCDO:0000147 Radha Raghupathy, Deepa Manwani, and Jane A. Little, “Iron Overload in Sickle Cell Disease,” Advances in Hematology, vol. 2010, Article ID 272940, 9 pages, 2010. doi:10.1155/2010/272940 MESH:D001803 Blood Transfusions The major and unavoidable complication of transfusions in sickle cell disease is iron overload. Transfusion is well-defined as prophylaxis (stroke) and as therapy (acute chest syndrome and stroke) for major complications of sickle cell disease and has been instituted, based on less conclusive data, for a range of additional complications, such as priapism, vaso-occlusive crises, leg ulcers, pulmonary hypertension, and during complicated pregnancies. Blood Transfusion SCDO:0000149 The distance from the sole to the crown of the head with body standing on a flat surface and fully extended. http://www.ebi.ac.uk/efo/EFO_0004339 Sufficient SCDO:0000149 EFO:0004339 Height Height/Length Length/Height Body Height SCDO:0000152 The mass or quantity of heaviness of an individual. It is expressed by units of pounds or kilograms. Add these terms from PhenX?: -- - Weight Loss/Gain Sufficient SCDO:0000152 MESH:D001835 Weight Body Weight SCDO:0000155 An abnormal hardening or increased density of bone tissue. Sufficient SCDO:0000155 Segen's Medical Dictionary. S.v. "bone sclerosis." Retrieved April 30 2019 from https://medical-dictionary.thefreedictionary.com/bone+sclerosis MESH:D010026 Bone Scleroses Osteoscleroses Osteosclerosis The bone is more radiopaque than normal on a plain film. deprecated-Bone Sclerosis true SCDO:0000156 A noninvasive method to assess the endothelial dysfunction in the brachial artery. Request inclusion into relevant ontology. http://en.wikipedia.org/wiki/Endothelial_dysfunction None BAUI Brachial Artery Ultrasound Imaging SCDO:0000161 Voltages between parts of the brain that are detectable with an electroencephalograph. Sufficient SCDO:0000161 CRISP:0487-1238 Brain Electrophysiological Activity Brain Oscillography EEG activity Brain Electrical Activity SCDO:0000162 An episode of severe pain that occurs with rapid onset even when pain-control medication is being used. Breakthrough pain can occur spontaneously or in relation to a specific activity, and can last from a few seconds to a few hours. Evidence-Based Management of Sickle Cell Disease: Expert Panel Report (EPR), 2014 Few but definitions not specific enough Evidence-Based Management of Sickle Cell Disease: Expert Panel Report (EPR), 2014 NCIT:C9203 There are currently no data that clearly describe or can be used to define breakthrough pain in SCD. Breakthrough Pain SCDO:0000163 The Brief IPQ has 9 items, 8 new items from the IPQ plus a causal question. All of the items except the causal question are rated using a 0-to-10-response scale. Five of the items assess Cognitive Illness Representations: Consequences (Item 1), Timeline (Item 2), Personal Control (Item 3), Treatment Control (Item 4), and Identity (Item 5). Two of the items assess Emotional Representations: Concern (Item 6) and Emotions (Item 8). One item assesses Illness Comprehensibility (Item 7). Assessment of the Causal Representation is by an open-ended response item adapted, which asks patients to list the three most important causal factors in their illness (Item 9). Responses to the causal item can be grouped into categories such as stress, lifestyle, hereditary, etc, determined by the particular illness studied, and categorical analysis can then be performed. Request inclusion into NCIT below "Research or Clinical Assessment Tool". Broadbent E, Petrie KJ, Main J, Weinman, J. (2006). The brief illness perception questionnaire. Journal of Psychosomatic Research, 60, 631-637. Multiple countries and cultural groups Self Clinic Patients Many Good psychometric properties, widely used, has been translated into several languages. Adults yes None Broadbent E, Petrie KJ, Main J, Weinman, J. (2006). The brief illness perception questionnaire. Journal of Psychosomatic Research, 60, 631-637. B-IPQ Brief Illness Perception Questionnaire Brief Illness Perception Questionnaire (B-IPQ) SCDO:0000164 Brief RCOPE is a 14-item instrument that measures religious coping with major life stressors. Responses on the Brief RCOPE indicate the frequency with which participants have used R/S coping behaviors on a Likert scale of 1 (not at all) to 4 (a great deal.) The scale has been used to examine positive and negative religious coping, including in teens with SCD. Request inclusion into NCIT below "Research or Clinical Assessment Tool". Pargament K, Koenig H, Perez L. The many methods of religious coping: development and initial validation of the RCOPE. J Clin Psychol. 2000;56:519-543. Self; Proxy (Parent report) Children with SCD and their parents. Demonstrated validity in SCD studies. Children and adults None SCDO Pargament K, Koenig H, Perez L. The many methods of religious coping: development and initial validation of the RCOPE. J Clin Psychol. 2000;56:519-543. Brief RCOPE SCDO:0000165 The improvement of forced expiratory volume in 1 second (FEV1) after inhalation of beta2-agonists and is typically measured as the change in airflow after the administration of short-acting beta2-adrenergic agonists (SABAs). Suggest that the description be updated in PhenX (https://www.phenxtoolkit.org/protocols/view/90301) Bauer S, Park HN, Seo HS, et al. Assessment of bronchodilator responsiveness following methacholine-induced bronchoconstriction in children with asthma. Allergy Asthma Immunol Res. 2011;3(4):245-50. Suggest update to description BDR Bronchodilator Responsiveness BDR SCDO:0000166 A test to assess an individual's change in pulmonary function in response to inhaled bronchodilator medications. Suggest update to label in PhenX (from "Bronchodilator Responsiveness (BDR)") Can also suggest inclusion in MESH below "Respiratory Function Tests" PhenX protocol: Bronchodilator Responsiveness (BDR) #90301 Suggest update to label phenX:90301 BDR Test Bronchodilator Responsiveness Testing Bronchodilator Responsiveness Test SCDO:0000182 A highly-sensitive (in the picomolar range, which is 10,000-fold more sensitive than conventional electrophoresis) and efficient technique that allows separation of proteins; nucleic acids; and carbohydrates. (Segen, Dictionary of Modern Medicine, 1992) http://purl.bioontology.org/ontology/MESH/D019075 Sufficient SCDO:0000182 MESH:D019075 Capillary Electrophoreses Capillary Zone Electrophoreses Capillary Zone Electrophoresis Capillary Electrophoresis SCDO:0000183 An instrument which, by means of a cathode-ray oscillograph, projects an electrocardiographic record on a luminous screen. Request inclusion into relevant ontology. http://encyclopedia2.thefreedictionary.com/cardioscope None Cardioscope SCDO:0000187 'Anatomical system that has as its parts the heart and blood vessels. [Curator team: []]' http://purl.obolibrary.org/obo/UBERON_0004535 UBERON:0004535 CV system deprecated Cardiovascular System true SCDO:0000188 'Clinical presentations that may be followed by evaluative studies that eventually lead to a diagnosis. [Curator team: []]' http://purl.bioontology.org/ontology/MESH/D002363 MESH:D002363 Case Histories Case Studies Case Study obsolete Case Reports true SCDO:0000189 Studies which start with the identification of persons with a disease of interest and a control (comparison, referent) group without the disease. The relationship of an attribute to the disease is examined by comparing diseased and non-diseased persons with regard to the frequency or levels of the attribute in each group. Suggest update to description in MESH http://purl.bioontology.org/ontology/MESH/D016022 Suggest update to description MESH:D016022 Case-Referrent Studies Case-Control Studies SCDO:0000190 A flexible, tubular device that is used to carry fluids into or from a blood vessel, hollow organ, or body cavity. Add info (rdfs:comment) about how catheters are used in different therapeutics. -- -- Link relevant Therapeutics term(s) to this term via "has medical device". http://purl.bioontology.org/ontology/MESH/D057785 Sufficient SCDO:0000190 MESH:D057785 Cannula Cannulas Catheters Catheter SCDO:0000191 A drug adverse event that is caused by a drug administration. Here a causal effect is established between the drug administration and the adverse event. Suggest definition replaced in OAE. Currenlty it's shown as the definition editor. http://purl.obolibrary.org/obo/OAE_0000095 Suggest update to description OAE:0000095 Causal Adverse Drug Event SCDO:0000192 A causal adverse drug event that is induced by a drug-drug interaction. http://purl.obolibrary.org/obo/OAE_0000179 Sufficient SCDO:0000192 OAE:0000179 Causal Adverse Drug Event Due to Drug-Drug Interaction SCDO:0000193 A causal adverse drug event that is induced by a food-drug interaction. http://purl.obolibrary.org/obo/OAE_0000180 Sufficient SCDO:0000193 OAE:0000180 Causal Adverse Drug Event Due to Food-Drug Interaction SCDO:0000194 A causal adverse drug event that is induced by genetic predisposition. Suggest small typo to be fixed in OAE. http://purl.obolibrary.org/obo/OAE_0000181 Suggest update to description OAE:0000181 Causal Adverse Drug Event Due to Genetic Predisposition SCDO:0000195 A causal adverse drug event due to genetic predisposition that is specifically induced by SNP. http://purl.obolibrary.org/obo/OAE_0000182 Sufficient SCDO:0000195 OAE:0000182 Causal Adverse Drug Event Due to SNP SCDO:0000198 The determination of the amount of free hemoglobin present in a sample. Suggest update to label in NCIT (from "Free Hemoglobin Measurement") Suggest update to label NCIT:C127617 Cell Free Hemoglobin Assay Cell Free Hemoglobin Blood Assay Cell Free Hemoglobin Test Free Hemoglobin Blood Test HGBFR Test Cell Free Hemoglobin Blood Test SCDO:0000199 The level of hemoglobin external to erythrocytes in a biological specimen. Request inclusion into relevant ontology If wanting to include "Plasma Hemoglobin Level" in the future, see CMO:0000588 for a description. synonyms: Plasma Free Hemoglobin (PFHb) Level, Plasma Hemoglobin Level. None SCDO (Jade Hotchkiss) Cell Free Haemoglobin Level Cell Free Hemoglobin Concentration Extracellular Hb Level Extracellular Hemoglobin Level HGBFR Level Cell Free Hemoglobin Level SCDO:0000206 Cerebral collateral circulation is a subsidiary vascular network which is dynamically recruited after arterial occlusion and may provide residual blood flow to ischemic areas. The description doesn't actually describe the term. Needs revision. Perhaps: Blood flow through cerebral collateral circulation, a subsidiary vascular network which is dynamically recruited after arterial occlusion and which may provide residual blood flow to ischemic areas. Suggest inclusion into CMO, below "circulation measurement". Cerebral collateral circulation in experimental ischemic stroke. Elisa Cuccione, Giada Padovano, Alessandro Versace, Carlo Ferrarese, Simone Beretta. Exp Transl Stroke Med. 2016; 8: 2. Published online 2016 Mar 1. doi: 10.1186/s13231-016-0015-0 PMCID: PMC4772465 None Cerebral Collateral Circulation Cerebral Collateral Flow SCDO:0000208 A test of how well the cerebrum is functioning. Request inclusion into relevant ontology. None SCDO (Jade Hotchkiss) Cerebral Function Test Cerebral Function Assay SCDO:0000213 The movement and the forces involved in the movement of the blood through the blood vessels in the brain. Request inclusion into relevant ontology. Perhaps replace with "cerebral blood flow measurement" from the EFO? None SCDO (Jade Hotchkiss) Cerebrovascular Hemodynamics SCDO:0000216 The analysis of a sample material, called an analyte, using a set of chemical procedures. Request inclusion into relevant ontology. http://www.reference.com/science/chemical-assay-80cfe6f498d34be5 None Chemical Assay SCDO:0000217 A medical imaging assessment of the chest wall, airways, lungs, pulmonary vessels, heart, mediastinum, and pleura. Sufficient SCDO:0000217 phenX:810201 Chest Radiograph Chest X-Ray SCDO:0000218 The Child Health Questionnaire (CHQ) is a family of general quality of life surveys that measures 14 unique physical and psychosocial concepts. The parent form is available in 2 lengths - the CHQ-PF50 and the CHQ-PF28. The child self-reported version of the CHQ consists of 87 items (CHQ-CF87). Multiple countries and cultural groups Self, Proxy Healthy Children; Children with Medical Conditions French, isiXhosa, isiZulu, Portuguese, Punjabi, Sesotho, Temil, Telugu, Gujarati Demonstrated validity with SCD populations; at least two publications using the measure in SCD. 5 to 18 years (child report 10 - 18 years; parent report 5 - 18 years) yes Few but definitions not specific enough SCDO Landgraf, J. M., Abetz, L., and Ware, J. E. (1996). Child health questionnaire (CHQ): A user's manual (1st Ed.). Boston, M.A.: The Health Institute, New England Medical Center. Panepinto JA, O'Mahar KM, DeBaun MR, Rennie KM, Scott JP. Validity of the child health questionnaire for use in children with sickle cell disease. J Pediatr Hematol Oncol. 2004 Sep;26(9):574-8. Wrotniak BH, Schall JI, Brault ME, Balmer DF, Stallings VA. Health-related quality of life in children with sickle cell disease using the child health questionnaire. J Pediatr Health Care. 2014 Jan-Feb;28(1):14-22. doi: 10.1016/j.pedhc.2012.09.004. Epub 2012 Nov 8. CHQ Child Health Questionnaire Child Health Questionnaire (CHQ) SCDO:0000219 A parent's highest level of education obtained, as reported by the child. Request inclusion into MESH below "Current Educational Attainment" (also to be suggested), below "Socioeconomic Factors". Also suggest inclusion in the EFO, below measurement. PhenX protocol: Child-Reported Parental Education Attainment #210201 Negligable phenX:210201 Child-Reported Parental Education Attainment SCDO:0000220 The CDI-2 is a 27-item self-report scale that helps to assess cognitive, affective and behavioral signs of depression in children and adolescents. Each item is scored on a scale from 0 to 2. Check and show which source was used for the description and whether the description was adapted from the source. Request inclusion into relevant ontology. Could be as a child of "Symptom Specific Assessment Tool" in the NCIT. Multiple countries and cultural groups Self Clinic Patients 7 to 17 years yes None Kovacs, M. (1985). The Children's Depression, Inventory (CDI). Psychopharmacology Bulletin, 21, 995-998. CDI 2 CDI-2 Children's Depression Inventory 2 Children's Depression Inventory-2 Children's Depression Inventory 2 (CDI 2) SCDO:0000221 A measure that seeks to determine the extent to which children and adolescents believe their own health-related behaviors will influence their health. It is a 20 item scale that contains 3 additional practice items and is a yes or no format. It contains 3 factors: belief in internality, belief in powerful others and belief in chance. There is a shorter 9-item version of the scale which is comparable to the full version and adapted for use in Egyptian children. Abdel Gawwad E, Ahmed MH, Kamal MM. Developing and testing of an Egyptian version of Children's Health Locus of Control scale. J Egypt Public Health Assoc. 1999; 74(1-2):139-73. Deaux EB. Health Locus of Control in Chukotka children. Alaska Med. 1992 Jul-Sep; 34(3):135-9. Parcel G.S. and Meyer M.P. (1978) Development of an instrument to measure children's health locus of control. Health Education Monographs, 6, 149-159. Multiple countries and cultural groups Self Healthy Children; Children with Medical Conditions English, Russian, a 9- item shorter Egyptian version Has adequate reliability, construct validity and internal consistency. Children and Adolescents no Few but definitions not specific enough CHLC Children's Health Locus of Control Scale Children's Health Locus of Control Scale (CHLC) SCDO:0000222 Surgical removal of the gallbladder. http://purl.bioontology.org/ontology/MESH/D002763 Sufficient SCDO:0000222 MESH:D002763 Cholecystectomies Cholecystectomy SCDO:0000225 A condition that co-exists or follows from sickle cell disease and that has a slow, creeping onset, slow progress and long continuance of disease manifestations. Probably too specific to warrant inclusion into anther ontology. Used info in "Evidence-Based Management of Sickle Cell Disease, Expert Panel Report, 2014" to link to relevant phenotypes. None SCDO http://purl.bioontology.org/ontology/MESH/Q000150 http://purl.obolibrary.org/obo/HP_0011010 Chronic Complications of Sickle Cell Disease SCDO:0000226 Chronic kidney disease (CKD) is defined as either having a glomerular filtration rate (GFR) of <60 mL/min/1.73 mL for >3 months with or without kidney damage or having evidence of kidney damage for 3 months, with or without decreased GFR. Suggest update to description in DO (currently no definition). NHLBI SCD New guidelines 2014. When assessed by albuminuria, often presents in second decade of life in sickle cell disease and prevalence increases with age. CKD is classified using a combination of GFR and ACR categories Sickle cell disease, hypertension, diabetes, polycystic kidney disease, glomerulonephritis, various other causes. Reduced glomerular filtration, elevated creatinine, anemia, bone disease, uremia. Few but definitions not specific enough SCDO NHLBI SCD New guidelines 2014. DOID:784 CKD Chronic Kidney Injury Chronic Renal Failure Evidence of kidney damage includes pathologic abnormalities or markers of kidney damage (i.e., proteinuria) independent of cause. Kidney disease severity is classified into five stages according to the level of GFR and presence of albuminuria. Chronic Kidney Disease SCDO:0000227 Is a long-term condition where the kidneys don't work as well as they should. There is conflicting positioning of this term in different ontologies. Need an expert to decide descriptions and positioning of this and related terms. CKD deprecated-Chronic Kidney Injury true SCDO:0000228 Chronic pain caused by damage to nerve fibers. It is usually associated with tissue injury. This pain is usually described as burning, numb, tingling, lancinating, shooting, or paroxysmal in nature and is associated with a sensation of pins and needles. Its severity is also enhanced by exposure to either cold or heat. Request inclusion into relevant ontology Evidence-Based Management of Sickle Cell Disease: Expert Panel Report (EPR), 2014 Few but definitions not freely available Chronic Neuropathic Pain SCDO:0000229 This pain occurs in a specific tissue or organ and is usually described as constant and deep, nagging, and achy in nature. Request inclusion into relevant ontology Evidence-Based Management of Sickle Cell Disease: Expert Panel Report (EPR), 2014 None Chronic Pain in a Specific Tissue or Organ SCDO:0000230 The only complaint is the patient's self-report of pain that does not go away. Request inclusion into relevant ontology Evidence-Based Management of Sickle Cell Disease: Expert Panel Report (EPR), 2014 http://doi.org/10.1182/blood-2012-04-383430 None Evidence-Based Management of Sickle Cell Disease: Expert Panel Report (EPR), 2014 Intractable Chronic Pain Without Obvious Pathology This type of chronic sickle cell pain may be an extension of recurrent acute painful episodes. Therefore, early and aggressive intervention in treating acute sickle cell pain may reduce the development of chronic pain. Chronic Pain often Unclear Etiology SCDO:0000232 Restrictive lung disease is a category of extrapulmonary, pleural, or parenchymal respiratory diseases that restrict lung expansion, resulting in a decreased lung volume, an increased work of breathing, and inadequate ventilation and/or oxygenation. Pulmonary function test demonstrates a decrease in the forced vital capacity. The description does not seem complete as it does not address the "chronic" aspect. Request inclusion into relevant ontology Wikipedia was used as the description source. Perhaps rather use NCIT's "Restrictive Lung Disease", and then use wikipedia as source for additional info. Did not find "Chronic Restrictive Lung Disease" in ontologies, but did find "Chronic Obstructive Lung Disease"...perhaps there was confusion between these terms when giving the name? None Chronic Restrictive Ventilatory Defect Restrictive Lung Disease Chronic Restrictive Lung Disease SCDO:0000233 Persistent pain in sickle cell disease. In sickle cell disease, persistent pain (pain that has lasted longer than 3 to 6 months) no longer serves as a warning sign. However, the time distinction is arbitrary and the condition may be difficult to distinguish from frequently recurring acute pain. Chronic pain may occur with objective signs of avascular necrosis, arthropathy, arthritis, leg ulcers or vertebral body collapse, or without objective signs, due to neuroplasticity of the peripheral nervous system. Request inclusion into relevant ontology SCD Management guidelines - Tanzania None SCDO Evidence-Based Management of Sickle Cell Disease: Expert Panel Report (EPR), 2014 SCD-Associated Chronic Pain Chronic Sickle Cell Pain SCDO:0000234 Sickle cell pain management that aims to restore function and improve the quality of life. Request inclusion into MESH below "Pain Management" / "Sickle Cell Pain Management" (also to be suggested for inclusion) None SCDO Chronic Sickle Cell Pain Treatment Chronic Sickle Cell Pain Management SCDO:0000235 An indication of a person's current cigarette use as well as some indication of cigarette smoking history. Request inclusion below "smoking status" in Exposure Ontology None SCDO (Jade Hotchkiss) Cigarette Smoking Status Measurement Cigarette Smoking Status SCDO:0000236 Meteorological conditions, including temperature, precipitation, and wind, that characteristically prevail in a particular region; includes regions of the earth having particular meteorological conditions. http://bioportal.bioontology.org/ontologies/CRISP?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FCSP%2F1035-6799 Sufficient SCDO:0000236 CRISP:1035-6799 Climate SCDO:0000245 Process of substituting a symbol or code for a term such as a diagnosis or procedure. (from Slee's Health Care Terms, 3d ed.) Add specific Sickle Cell Disease related codes as instances/individuals below *Clinical Coding*? (see ICD-10 codes here: www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-) http://purl.bioontology.org/ontology/MESH/D059019 Sufficient SCDO:0000245 MESH:D059019 Coding Medical Coding Clinical Coding SCDO:0000246 The capability to perform acceptably those duties directly related to patient care. http://purl.bioontology.org/ontology/MESH/D002983 Sufficient SCDO:0000246 MESH:D002983 Clinical Competencies Clinical Competency Clinical Skill Competencies, Clinical Competency, Clinical Skill, Clinical Skills, Clinical Clinical Competence SCDO:0000247 'Work that consists of a conference of physicians on their observations of a patient at the bedside, regarding the physical state, laboratory and other diagnostic findings, clinical manifestations, results of current therapy, etc. A clinical conference usually ends with a confirmation or correction of clinical findings by a pathological diagnosis performed by a pathologist. Clinical conference is often referred to as a clinico-pathological conference. [Curator team: []]' http://purl.bioontology.org/ontology/MESH/D016429 MESH:D016429 Clinico-Pathologic Conference Clinico-Pathological Conference obsolete Clinical Conference true SCDO:0000249 'A quick and accurate way of assessing the patient health states using well defined set of questions and analyzed for an optimal clinical decision for the patient. [Curator team: Gaston K. Mazandu]' obsolete Clinical Diagnostic Questionnaire true SCDO:0000250 A physician administered examination to assess peripheral neuropathy. PhenX protocol: Neuropathy - Clinical Assessment #130201 Can be used to assess the severity of symptoms and disability associated with peripheral neuropathy caused by a number of disorders including tumors, infections, autoimmune diseases, and inherited disorders such as Charcot-Marie-Tooth disease. Sufficient SCDO:0000250 phenX:130201 Charcot-Marie-Tooth Neuropathy Score Neuropathy - Clinical Assessment Clinical Neuropathy Assessment SCDO:0000251 Abnormal clinical manifestations of beta thalassemia that are as a result of the underlying genotype. Could this not rather be "Clinical Subtype of Beta Thalassemia"? See "clinical subtype" in Orphanet. Request inclusion into relevant ontology None SCDO (Clair Ingram) Clinical Phenotype of Beta Thalassemia SCDO:0000252 'A work that reports on the results of a research study to evaluate interventions or exposures on biomedical or health-related outcomes. The two main types of clinical studies are interventional studies (clinical trials) and observational studies. While most clinical studies concern humans, this publication type may be used for clinical veterinary articles meeting the requisites for humans. [Curator team: []]' http://purl.bioontology.org/ontology/MESH/D000068397 MESH:D000068397 obsolete Clinical Study true SCDO:0000253 Works about research studies that evaluate interventions or exposures on biomedical or health-related outcomes. The two main types of clinical studies are interventional studies (clinical trials) and observational studies. Term to be adapted as necessary to match EDDA Study Designs Taxonomy http://purl.bioontology.org/ontology/MESH/D000068456 Sufficient SCDO:0000253 MESH:D000068456 Clinical Studies as Topic SCDO:0000254 'A work that reports on the results of a clinical study in which participants are assigned to receive one or more interventions so that researchers can evaluate the interventions on biomedical or health-related outcomes. The assignments are determined by the study protocol. Participants may receive diagnostic, therapeutic, or other types of interventions. While most clinical trials concern humans, this publication type may be used for clinical veterinary articles meeting the requisites for humans. [Curator team: []]' http://purl.bioontology.org/ontology/MESH/D016430 MESH:D016430 Intervention Study obsolete Clinical Trial true SCDO:0000255 'Work that is the report of a pre-planned, usually controlled, clinical study of the safety and efficacy of diagnostic, therapeutic, or prophylactic drugs, devices, or techniques based on a small number of healthy persons and conducted over the period of about a year in either the United States or a foreign country. [Curator team: []]' http://purl.bioontology.org/ontology/MESH/D017426 MESH:D017426 Clinical Trial, Phase 1 obsolete Clinical Trial, Phase I true SCDO:0000256 'Work that is a report of a pre-planned, usually controlled, clinical study of the safety and efficacy of diagnostic, therapeutic, or prophylactic drugs, devices, or techniques based on several hundred volunteers, including a limited number of patients, and conducted over a period of about two years in either the United States or a foreign country. [Curator team: []]' http://purl.bioontology.org/ontology/MESH/D017427 MESH:D017427 Clinical Trial, Phase 2 obsolete Clinical Trial, Phase II true SCDO:0000257 'Work that is a report of a planned post-marketing study of diagnostic, therapeutic, or prophylactic drugs, devices, or techniques that have been approved for general sale after clinical trials, phases I, II, and III. These studies, conducted in the United States or a foreign country, often garner additional data about the safety and efficacy of a product. [Curator team: []]' http://purl.bioontology.org/ontology/MESH/D017429 MESH:D017429 Clinical Trial, Phase 4 obsolete Clinical Trial, Phase IV true SCDO:0000258 'Work that is a report of a pre-planned, usually controlled, clinical study of the safety and efficacy of diagnostic, therapeutic, or prophylactic drugs, devices, or techniques after phase II trials. A large enough group of patients is studied and closely monitored by physicians for adverse response to long-term exposure, over a period of about three years in either the United States or a foreign country. [Curator team: []]' http://purl.bioontology.org/ontology/MESH/D017428 MESH:D017428 Clinical Trial, Phase 3 obsolete Clinical Trial, Phase III true SCDO:0000259 Works about pre-planned studies of the safety, efficacy, or optimum dosage schedule (if appropriate) of one or more diagnostic, therapeutic, or prophylactic drugs, devices, or techniques selected according to predetermined criteria of eligibility and observed for predefined evidence of favorable and unfavorable effects. This concept includes clinical trials conducted both in the U.S. and in other countries. http://purl.bioontology.org/ontology/MESH/D002986 Sufficient SCDO:0000259 MESH:D002986 Clinical Trials as Topic SCDO:0000262 A direct form of psychotherapy based on the interpretation of situations (cognitive structure of experiences) that determine how an individual feels and behaves. It is based on the premise that cognition, the process of acquiring knowledge and forming beliefs, is a primary determinant of mood and behavior. The therapy uses behavioral and verbal techniques to identify and correct negative thinking that is at the root of the aberrant behavior. http://purl.bioontology.org/ontology/MESH/D015928 Sufficient SCDO:0000262 MESH:D015928 CBT Cognition Therapies Cognition Therapy Cognitive Behavioral Therapies Cognitive Behavioral Therapy Cognitive Behaviour Therapy Cognitive Psychotherapies Cognitive Psychotherapy Cognitive Therapies Cognitive Therapy SCDO:0000263 Studies in which subsets of a defined population are identified. These groups may or may not be exposed to factors hypothesized to influence the probability of the occurrence of a particular disease or other outcome. Cohorts are defined populations which, as a whole, are followed in an attempt to determine distinguishing subgroup characteristics. http://purl.bioontology.org/ontology/MESH/D015331 Sufficient SCDO:0000263 MESH:D015331 Cohort Analyses Cohort Studies SCDO:0000265 A profound state of unconsciousness associated with depressed cerebral activity from which the individual cannot be aroused. Coma generally occurs when there is dysfunction or injury involving both cerebral hemispheres or the brain stem reticular formation. The specific type of Blood Test (s) used to diagnose a coma should be specified. -- -- Named Individual removed (is diagnosed by): -- As in any neurologic condition, history and examination form the cornerstone of diagnosis when the patient is in a coma; however, history must be obtained from family, friends, or EMS. The Glasgow Coma Scale is a system of examining a comatose patient. It is helpful for evaluating the depth of the coma, tracking the patient's progress, and predicting (somewhat) the ultimate outcome of the coma. The Glasgow Coma Scale assigns a different number of points for exam results in three different categories: opening the eyes, verbal response (using words or voice to respond), and motor response (moving a part of the body). Fifteen is the largest possible number of total points, indicating the highest level of functioning. The highest level of functioning would be demonstrated by an individual who spontaneously opens his/her eyes, gives appropriate answers to questions about his/her situation, and can carry out a command (such as "move your leg" or "nod your head"). Three is the least possible number of total points and would be given to a patient for whom not even a painful stimulus is sufficient to provoke a response. In the middle are those patients who may be able to respond, but who require an intense or painful stimulus, and whose response may demonstrate some degree of brain malfunctioning (such as a person whose only response to pain in a limb is to bend that limb in toward the body). When performed as part of the admission examination, a Glasgow score of three to five points often suggests that the patient has likely suffered fatal brain damage, while eight or more points indicates that the patient's chances for recovery are good. Expansion of the pupils and respiratory pattern are also important. Metabolic causes of coma are diagnosed from blood work and urinalysis to evaluate blood chemistry, drug screen, and blood cell abnormalities that may indicate infection. Anatomic causes of coma are diagnosed from CT (computed tomography) or MRI (magnetic resonance imaging) scans. http://purl.bioontology.org/ontology/MESH/D003128 Sufficient SCDO:0000265 MESH:D003128 Comas Coma SCDO:0000267 A co-existing or additional disease with reference to an initial diagnosis or with reference to the index condition that is the subject of study. Request inclusion into relevant ontology As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Joseph Telfair -- Include here: -- Asthma -- Osteonecrosis of the Femoral Head -- Restrictive Lung Disease (currently Chronic Restrictive Lung Disease in SCDO) -- Retinopathy -- Cardiac Dysfunction -- Renal Dysfunction/Renal Failure -- -- ...and others Few but definitions not freely available SCDO (Jade Hotchkiss) Additional Disease Co-Existing Disease Co-Morbid Condition Co-Morbid Disease Comorbid Disease SCDO:0000268 Comparison of outcomes, results, responses, etc for different techniques, therapeutic approaches or other inputs. http://purl.bioontology.org/ontology/MESH/D003160 Sufficient SCDO:0000268 MESH:D003160 Comparative Studies Comparative Study SCDO:0000271 Therapeutic practices which are not currently considered an integral part of conventional allopathic medical practice. They may lack biomedical explanations but as they become better researched some (physical therapy modalities; diet; acupuncture) become widely accepted whereas others (humors, radium therapy) quietly fade away, yet are important historical footnotes. Therapies are termed as Complementary when used in addition to conventional treatments and as Alternative when used instead of conventional treatment. Year introduced: 2002(1986). http://purl.bioontology.org/ontology/MESH/D000529 Sufficient SCDO:0000271 MESH:D000529 Complementary Medicine Complementary Therapy SCDO:0000272 'Compound heterozygosity in medical genetics is the condition of having two heterogeneous recessive alleles at a particular locus that can cause genetic disease in a heterozygous state. [Curator team: []]' obsolete Compound Heterozygous Hemoglobinopathy true SCDO:0000276 Dark red, comma- or corkscrew-shaped vascular fragment that appears to be isolated from neighboring blood vessels in the conjunctiva. Normally benign, this lesion can serve as the first diagnostic sign of sickle cell retinopathy. The conjunctival comma sign results from transient vaso-occlusive processes in the microvasculature of bulbar conjunctiva. It is not seen in sickle trait, but is common in SCD. Request inclusion into relevant ontology. Ballas et al 2010 Am J Hematol None Conjunctival Comma Sign SCDO:0000277 'A work that consists of summary statements representing the majority and current agreement of physicians, scientists, and other professionals meeting to reach a consensus on a selected subject. [Curator team: []]' http://purl.bioontology.org/ontology/MESH/D016446 MESH:D016446 obsolete Consensus Development Conference true SCDO:0000278 'Work consisting of summary statements, from a conference sponsored by NIH, representing the majority of current opinion of physicians, scientists, and other professionals on a selected subject. [Curator team: []]' http://purl.bioontology.org/ontology/MESH/D016447 MESH:D016447 NIH Consensus Development Conference obsolete Consensus Development Conference, NIH true SCDO:0000280 A tool for collecting standardized information on enrollees' experiences with health plans and their services. Request inclusion into NCIT below "Research or Clinical Assessment Tool". PhenX protocol: Quality of Care - Children #820102 Proxy (Primary caregiver) Used to assess the patient-reported health care needs and quality of service from health care providers for individuals with chronic conditions such as sickle cell disease (SCD). Children and adolescents, ages 17 and younger yes None PhenX:820102 This measure includes general questions about access to care and quality of care and additional questions about the services provided to children with chronic conditions. Items CC1-CC38 of the questionnaire are version 4.0 of the Children with Chronic Conditions Item Set. Consumer Assessment of Healthcare Providers and Systems (CAHPS) Health Plan Survey 4.0 Child Medicaid Questionnaire SCDO:0000282 A study in which observations are made before and after an intervention, both in a group that receives the intervention and in a control group that does not. http://purl.bioontology.org/ontology/MESH/D065187 Sufficient SCDO:0000282 MESH:D065187 Controlled Before-After Studies Controlled Pre-Post Studies SCDO:0000283 'A work that reports on a clinical trial involving one or more test treatments, at least one control treatment, specified outcome measures for evaluating the studied intervention, and a bias-free method for assigning patients to the test treatment. The treatment may be drugs, devices, or procedures studied for diagnostic, therapeutic, or prophylactic effectiveness. Control measures include placebos, active medicine, no-treatment, dosage forms and regimens, historical comparisons, etc. When randomization using mathematical techniques, such as the use of a random numbers table, is employed to assign patients to test or control treatments, the trial is characterized as a randomized controlled trial. [Curator team: []]' http://purl.bioontology.org/ontology/MESH/D018848 MESH:D018848 obsolete Controlled Clinical Trial true SCDO:0000284 Works about clinical trials involving one or more test treatments, at least one control treatment, specified outcome measures for evaluating the studied intervention, and a bias-free method for assigning patients to the test treatment. The treatment may be drugs, devices, or procedures studied for diagnostic, therapeutic, or prophylactic effectiveness. Control measures include placebos, active medicines, no-treatment, dosage forms and regimens, historical comparisons, etc. When randomization using mathematical techniques, such as the use of a random numbers table, is employed to assign patients to test or control treatments, the trials are characterized as randomized controlled trials as topic. http://purl.bioontology.org/ontology/MESH/D018849 Sufficient SCDO:0000284 MESH:D018849 Controlled Clinical Trials as Topic SCDO:0000286 A state of harmony between internal needs and external demands and the processes used in achieving this condition. http://purl.bioontology.org/ontology/MESH/D000223 Sufficient SCDO:0000286 MESH:D000223 Adaptive Behavior Adaptive Behaviors Coping Behavior Coping Behaviors Coping Skills Psychologic Adaptation Psychological Adaptation Coping Skill SCDO:0000287 The CSQ-SCD consists of 78 items, which make up seven scales related to coping with pain in general: Diverting attention, Reinterpreting pain sensations, Calming self-statements, Ignoring pain sensations, Praying and hoping, Catastrophising, and Increasing activity level; together with six scales developed as specifically relevant to sickle cell disease: Fear self-statements, Anger self-statements, Isolation, Taking fluids, Resting, and Heat/cold/massage. Patients rated their use of each response from 0 = never to 6 = always, and scores were averaged to produce a mean for each scale. Two additional aspects were assessed by single items: perceived ability to control pain was rated from 0 = no control to 6 = complete control, and perceived ability to decrease pain was rated from 0 = can't decrease it at all to 6 = can decrease it completely. Request inclusion into NCIT below "Research or Clinical Assessment Tool". Abrams M.R., Phillips G. and Keefe F.J. (1989). Sickle cell disease pain: Relation of coping strategies Multiple countries and cultural groups Self Adults with SCD Demonstrated validity with SCD populations USA and UK; several publications. Adults None Gil K.M., Abrams M.R., Phillips G. and Keefe F.J. (1989). Sickle cell disease pain: Relation of coping strategies to adjustment. Journal of Consulting and Clinical Psychology, 57, 725-731. CSQ-SCD Coping Strategies Questionnaire revised for Sickle Cell Disease Coping Strategies Questionnaire revised for Sickle Cell Disease (CSQ-SCD) SCDO:0000288 The CSQ-SCD consists of 78 items, which make up seven scales related to coping with pain in general: Diverting attention, Reinterpreting pain sensations, Calming self-statements, Ignoring pain sensations, Praying and hoping, Catastrophising, and Increasing activity level; together with six scales developed as specifically relevant to sickle cell disease: Fear self-statements, Anger self-statements, Isolation, Taking fluids, Resting, and Heat/cold/massage. Patients rated their use of each response from 0 = never to 6 = always, and scores were averaged to produce a mean for each scale. Two additional aspects were assessed by single items: perceived ability to control pain was rated from 0 = no control to 6 = complete control, and perceived ability to decrease pain was rated from 0 = can't decrease it at all to 6 = can decrease it completely. Request inclusion into NCIT below "Research or Clinical Assessment Tool". Gil K.M., Williams D.A., Thompson, R.J. and Kinney, T.R. (1991). Sickle cell disease in children and adolescents: The relation of child and parent pain coping strategies to adjustment. Journal of Pediatric Psychology, 16, 643-663. Multiple countries and cultural groups Self Children with SCD Demonstrated validity with SCD populations USA and UK; several publications. Children None Gil K.M., Williams D.A., Thompson, R.J. and Kinney, T.R. (1991). Sickle cell disease in children and adolescents: The relation of child and parent pain coping strategies to adjustment. Journal of Pediatric Psychology, 16, 643-663. CSQ-SCD Children Coping Strategies Questionnaire revised for Sickle Cell Disease Children (CSQ-SCD Children) SCDO:0000291 A causal adverse drug event that is induced by a corticosteroid. Request inclusion into OAE below "Causal Adverse Drug Event". None SCDO (Jade Hotchkiss) Corticosteroid-Induced Adverse Event SCDO:0000292 A corticosteroid-induced adverse event that has the outcome of vaso-occlusion. Request inclusion into OAE below "Corticosteroid-Induced Adverse Event" (also suggested by us for inclusion). None SCDO (Jade Hotchkiss) Corticosteroid-Induced Vaso-Occlusive Adverse Event SCDO:0000294 The personal cost of disease which may be economic, social, or psychological. The cost of illness may be reflected in absenteeism, productivity, response to treatment, peace of mind, or quality of life. It differs from health care costs, the societal cost of providing services related to the delivery of health care. http://purl.bioontology.org/ontology/MESH/D017281 Sufficient SCDO:0000294 MESH:D017281 Burden of Illness Cost of Disease Cost of Sickness Costs of Disease Disease Cost Disease Costs Economic Burden of Disease Sickness Cost Cost of Illness SCDO:0000295 The extent to which a health intervention can be regarded as providing value for money, based on a cost-effectiveness analysis that compares the costs and health effects of the intervention. This informs decision-makers who have to determine where to allocate limited healthcare resources. Request inclusion into relevant ontology, possibly into MESH, perhaps in an appropriate place below "Quality of Health Care". http://www.medicine.ox.ac.uk/bandolier/painres/download/whatis/Cost-effect.pdf Negligable Health Care Economics Health Economics Cost-Effectiveness of Healthcare SCDO:0000296 A bioassay to measure the serum concentration of creatinine, a metabolite of muscle creatine that is filtered out of blood by the kidneys. Sufficient SCDO:0000296 phenX:141400 Blood Creatinine Assay Blood Creatinine Test Serum Creatinine Serum Creatinine Assay Creatinine Blood Test SCDO:0000297 Brief therapeutic approach which is ameliorative rather than curative of acute psychiatric emergencies. Used in contexts such as emergency rooms of psychiatric or general hospitals, or in the home or place of crisis occurrence, this treatment approach focuses on interpersonal and intrapsychic factors and environmental modification. (APA Thesaurus of Psychological Index Terms, 7th ed) http://purl.bioontology.org/ontology/MESH/D003419 Sufficient SCDO:0000297 MESH:D003419 Crisis Interventions Interventions, Crisis Crisis Intervention SCDO:0000298 Studies in which the presence or absence of disease or other health-related variables are determined in each member of the study population or in a representative sample at one particular time. This contrasts with longitudinal studies which are followed over a period of time. http://purl.bioontology.org/ontology/MESH/D003430 Sufficient SCDO:0000298 MESH:D003430 Cross-Sectional Analysis Cross-Sectional Study Cross-Sectional Studies SCDO:0000299 A collective expression for all behaviour patterns acquired and socially transmitted through symbols. Culture includes customs, traditions, and language. http://purl.bioontology.org/ontology/MESH/D003469 Sufficient SCDO:0000299 MESH:D003469 Cultural Beliefs Cultural Values Culture SCDO:0000301 Therapeutics relating to or used in the cure of diseases. Request inclusion into relevant ontology None SCDO http://www.merriam-webster.com/dictionary/curative Curative Therapeutics SCDO:0000304 The length of time that a person has lived since their birth up until the current day. Few but available definitions not adequate SCDO (Jade Hotchkiss) Current Chronological Age Current Age SCDO:0000305 The respondent's highest level of education at the current time. Request inclusion into MESH below "Socioeconomic Factors". Few but definitions not freely available Educational Attainment Current Educational Attainment SCDO:0000306 The respondent's current employment status. PhenX protocol: Current Employment Status #11301 Sufficient SCDO:0000306 phenX:11301 Employment Status Current Employment Status SCDO:0000307 The respondent's current marital status. Can add sub-classes of "Marital Status" from MESH. PhenX protocol: Current Marital Status #10902 Sufficient SCDO:0000307 phenX:10902 Marital Status Marital or Partnership Status Current Marital Status SCDO:0000310 The amount of the protein cystatin C (formerly gamma trace, post-gamma-globulin or neuroendocrine basic polypeptide) found in a specified sample of blood. This extracellular cystatin subtype is abundantly expressed in bodily fluids. This class is used as a biomarker of kidney function and kidney disease. http://purl.bioontology.org/ontology/MESH/D055316 http://www.ebi.ac.uk/efo/EFO_0004617 Suggest update to description in CMO CMO:0002777 Blood CC Level Cystatin 3 Level Gamma Trace Level Gamma-Trace Level Neuroendocrine Basic Polypeptide Level Post Gamma Globulin Level Post-Gamma-Globulin Level Blood Cst3 Level Blood Cystatin C Level SCDO:0000311 A blood disorder characterized by the appearance of sickle-shaped red blood cells and anemia. http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57- Sufficient SCDO:0000311 ICD10CM:D57 D57 D57 Sickle-Cell Disorders SCDO:0000312 Broad term used to describe several different acute conditions occurring with sickle cell disease, including aplastic crisis, hemolytic crisis, and vasoocclusive crisis. http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.0 Sufficient SCDO:0000312 ICD10CM:D57.0 D57.0 Hb-SS disease with vasoocclusive pain Sickle cell anemia with crisis Sickle cell anemia with vasoocclusive pain D57.0 Hb-SS disease with crisis SCDO:0000313 - Few but definitions not available http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.01 ICD10CM:D57.01 D57.01 Hb-SS disease with acute chest syndrome Sickle cell anemia with acute chest syndrome Sickle cell anemia, acute chest syndrome D57.01 Hb-SS disease with acute chest syndrome SCDO:0000314 - Few but definitions not available http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.02 ICD10CM:D57.02 Acute sickle cell splenic sequestration crisis D57.02 Hb-SS disease with splenic sequestration Sickle cell anemia acute crisis splenic sequestration D57.02 Hb-SS disease with splenic sequestration SCDO:0000315 - Few but definitions not freely available http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.1 ICD10CM:D57.1 D57.1 Sickle cell anemia without crisis Sickle-cell disease without crisis D57.1 Sickle-cell disease without crisis SCDO:0000316 One of the sickle cell disorders characterized by the presence of both hemoglobin s and hemoglobin c. It is similar to, but less severe than sickle cell anemia. http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.2 Sufficient SCDO:0000316 ICD10CM:D57.2 D57.2 D57.2 Sickle-cell/Hb-C disease SCDO:0000317 - Few but definitions not freely available http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.20 ICD10CM:D57.20 D57.20 Sickle Cell Disease-SC without crisis Sickle-cell/Hb-C disease without crisis D57.20 Sickle-cell/Hb-C disease without crisis SCDO:0000318 - Few but definitions not freely available http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.21 ICD10CM:D57.21 D57.21 Sickle Cell Disease-SC with crisis Sickle-cell/Hb-C disease with crisis D57.21 Sickle-cell/Hb-C disease with crisis SCDO:0000319 - Few but definitions not freely available http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.211 ICD10CM:D57.211 Acute chest syndrome due to sickle cell-hemoglobin c disease crisis Acute chest syndrome sickle cell hb-c crisis D57.211 Sickle Cell Disease-SC with acute chest syndrome Sickle-cell/Hb-C disease with acute chest syndrome D57.211 Sickle-cell/Hb-C disease with acute chest syndrome SCDO:0000320 - Few but definitions not freely available http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.212 ICD10CM:D57.212 D57.212 Sickle Cell Disease-SC with splenic sequestration Sickle-cell/Hb-C disease with splenic sequestration D57.212 Sickle-cell/Hb-C disease with splenic sequestration SCDO:0000321 - Few but definitions not freely available http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.219 ICD10CM:D57.219 D57.219 Sickle Cell Disease-SC with crisis NOS Sickle Cell Disease-SC with crisis, unspecified Sickle Cell Disease-SC with vasoocclusive pain NOS Sickle cell-hemoglobin c disease with crisis Sickle-cell/Hb-C disease with crisis NOS Sickle-cell/Hb-C disease with crisis, unspecified Sickle-cell/Hb-C disease with vasoocclusive pain NOS D57.219 Sickle-cell/Hb-C disease with crisis, unspecified SCDO:0000322 The condition of being heterozygous for hemoglobin S. http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.3 Sufficient SCDO:0000322 ICD10CM:D57.3 D57.3 D57.3 Sickle-cell trait SCDO:0000323 Hemolytic anemia, in which patients are heterozygous for both the sickle cell gene and a thalassemia gene. http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.4 Sufficient SCDO:0000323 ICD10CM:D57.4 D57.4 D57.4 Sickle-cell thalassemia SCDO:0000324 - Few but definitions not freely available http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.40 ICD10CM:D57.40 D57.40 D57.40 Sickle-cell thalassemia without crisis SCDO:0000325 - Few but definitions not freely available http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.41 ICD10CM:D57.41 D57.41 Sickle-cell thalassemia with (painful) crisis Sickle-cell thalassemia with crisis Sickle-cell thalassemia with vasoocclusive pain D57.41 Sickle-cell thalassemia, unspecified, with crisis SCDO:0000326 - Few but definitions not freely available http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.411 ICD10CM:D57.411 D57.411 Sickle-cell thalassemia, unspecified, with acute chest syndrome D57.411 Sickle-cell thalassemia, unspecified, with acute chest syndrome SCDO:0000327 - Few but definitions not freely available http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.412 ICD10CM:D57.412 D57.412 Sickle cell thalassemia with splenic sequestration Sickle-cell thalassemia, unspecified, with splenic sequestration D57.412 Sickle-cell thalassemia, unspecified, with splenic sequestration SCDO:0000328 - Few but definitions not freely available http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.419 ICD10CM:D57.419 D57.419 Sickle-cell thalassemia with (painful) crisis NOS Sickle-cell thalassemia with vasoocclusive pain NOS Sickle-cell thalassemia, unspecified, with crisis D57.419 Sickle-cell thalassemia, unspecified, with crisis SCDO:0000329 - Few but definitions not freely available http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.8 ICD10CM:D57.8 D57.8 Other sickle-cell disorders D57.8 Other sickle-cell disorders SCDO:0000330 - Few but definitions not freely available http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.80 ICD10CM:D57.80 D57.80 D57.80 Other sickle-cell disorders without crisis SCDO:0000331 - Few but definitions not freely available http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.81 ICD10CM:D57.81 D57.81 D57.81 Other sickle-cell disorders with crisis SCDO:0000332 - Few but definitions not freely available http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.811 ICD10CM:D57.811 D57.811 D57.811 Other sickle-cell disorders with acute chest syndrome SCDO:0000333 - Few but definitions not freely available http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.812 ICD10CM:D57.812 D57.812 D57.812 Other sickle-cell disorders with splenic sequestration SCDO:0000334 - Few but definitions not freely available http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.819 ICD10CM:D57.819 D57.819 D57.819 Other sickle-cell disorders with crisis, unspecified SCDO:0000338 'Protein molecule are large, complex molecules that play many critical roles in the body. They do most of the work in cells and are required for the structure, function, and regulation of the body's tissues and organs. [Curator team: []]' https://ghr.nlm.nih.gov/primer/howgeneswork/protein obsolete Protein Molecule true SCDO:0000343 A form of beta-thalassemia characterized by decreased or absent synthesis of the delta- and beta-globin chains with a compensatory increase in expression of fetal gamma-chain synthesis. Sufficient SCDO:0000343 ORPHA:231237 Delta Beta Thalassaemia Delta-Beta-Thalassaemia Delta-Beta-Thalassemia F Thalassaemia Delta Beta Thalassemia SCDO:0000344 A hereditary disorder characterized by reduced or absent delta-globin thus effecting the level of hemoglobin A2, a minor component of adult hemoglobin monitored in the diagnosis of beta-thalassemia. http://purl.bioontology.org/ontology/MESH/D055538 Sufficient SCDO:0000344 MESH:D055538 Delta Thalassaemia Delta Thalassaemias Delta Thalassemias Delta-Thalassaemia Delta-Thalassaemias Delta-Thalassemia Delta Thalassemia SCDO:0000346 An acute febrile disease transmitted by the bite of AEDES mosquitoes infected with Dengue Virus. It is self-limiting and characterized by fever, myalgia, headache, and rash. Severe Dengue is a more virulent form of dengue. http://purl.bioontology.org/ontology/MESH/D003715 Sufficient SCDO:0000346 MESH:D003715 Break Bone Fever Break-Bone fever Breakbone Fever Dengue Dengue Fever SCDO:0000347 'The system pertaining to teeth, oral cavity, and associated structures. [Curator team: []]' http://medical-dictionary.thefreedictionary.com/dentistry deprecated Dental System true SCDO:0000359 Terms that are no longer being used in the ontology. deprecated terms SCDO:0000360 A common mental disorder, characterized by sadness, hopelessness, loss of interest or pleasure, feelings of guilt or low self-worth, disturbed sleep or appetite, feelings of tiredness, and poor concentration. Depression can be long-lasting or recurrent, substantially impairing an individual's ability to function at work or school or cope with daily life. http://www.who.int/topics/depression/en/ Sufficient SCDO:0000360 SIO:000824 Depressive Symptoms Low Mood Depression SCDO:0000365 Skill in performing tasks, especially with the hands. Request inclusion into relevant ontology http://en.oxforddictionaries.com/definition/dexterity Few but definitions not freely available SCDO Dexterity SCDO:0000376 A medical device used to diagnose medical conditions. http://purl.obolibrary.org/obo/ERO_0001448 Sufficient SCDO:0000376 ERO:0001448 Diagnostic Device SCDO:0000379 Diagnostic tools (including the instruments, laboratory assays and methods of patient examination) used for differential diagnosis, the measurements obtained using these tools, and the diagnostic devices used in obtaining the measurements. Request inclusion into relevant ontology. None SCDO (Jade Hotchkiss) Diagnostics SCDO:0000380 A non-steroidal anti-inflammatory agent (NSAID) with antipyretic and analgesic actions. It is primarily available as the sodium salt. Sufficient SCDO:0000380 MESH:D004008 2-((2,6-dichlorophenyl)amino)benzeneacetic acid Diclofenac Acid Orthofen [2-(2,6-dichloroanilino)phenyl]acetic acid Diclofenac SCDO:0000382 Concepts involved with nutritional physiology, including categories of substances eaten for sustenance, nutritional phenomena and processes, eating patterns and habits, and measurable nutritional parameters. Should this term rather be replaced by more specific terms such as Dietary Intake? Or have such terms as sub-classes? http://purl.bioontology.org/ontology/MESH/D000066888 Sufficient SCDO:0000382 MESH:D000066888 Diet, Food, and Nutrition SCDO:0000383 obsolete Diffusion Capacity by Biochemical Methods true SCDO:0000384 The amount of a gas taken up, by the pulmonary capillary blood from the alveolar gas, per minute per unit of average pressure of the gradient of the gas across the blood-air barrier. http://purl.bioontology.org/ontology/MESH/D011653 Sufficient SCDO:0000384 MESH:D011653 Alveolar membrane diffusion capacity DL Diffusing Capacity Membrane diffusion capacity Pulmonary Diffusing Capacity Diffusion Capacity of Lung SCDO:0000385 Clinical assessment to determine the capacity of an individual's lung to exchange gases (e.g., oxygen and carbon dioxide) across the alveolar-capillary interface. Suggest update to label in PhenX (from "Lung Function - Diffusion Capacity") Need to add equipment used for this test under "Devices" and link to them below. PhenX protocol: Lung Function - Diffusion Capacity #810301 Suggest update to label phenX:810301 Pulmonary Diffusing Capacity Test Diffusion Capacity Test SCDO:0000386 One DALY can be thought of as one lost year of "healthy" life. The sum of these DALYs across the population, or the burden of disease, can be thought of as a measurement of the gap between current health status and an ideal health situation where the entire population lives to an advanced age, free of disease and disability. Multiple countries and cultural groups Self; Proxy All WHO Global Burden of Disease assessment, also used in SCD studies Children and adults no Few but definitions not specific enough DALY Disability-Adjusted Life Year Calculation: DALY = YLL + YLD - The YLL basically correspond to the number of deaths multiplied by the standard life expectancy at the age at which death occurs. The basic formula for YLL (without yet including other social preferences discussed below), is the following for a given cause, age and sex: YLL = N x L where: N = number of deaths L = standard life expectancy at age of death in years. Because YLL measure the incident stream of lost years of life due to deaths, an incidence perspective has also been taken for the calculation of YLD in the original Global Burden of Disease Study for year 1990 and in subsequent WHO updates for years 2000 to 2004. To estimate YLD for a particular cause in a particular time period, the number of incident cases in that period is multiplied by the average duration of the disease and a weight factor that reflects the severity of the disease on a scale from 0 (perfect health) to 1 (dead). The basic formula for YLD is the following (again, without applying social preferences): YLD = I x DW x L where: I = number of incident cases; DW = disability weight; L = average duration of the case until remission or death (years). Prevalence YLD - The recent GBD 2010 study published by IHME in December 2012 used an updated life expectancy standard for the calculation of YLL and based the YLD calculation on prevalence rather than incidence: YLD = P x DW where: P = number of prevalent cases; DW = disability weight. Disability-Adjusted Life Year (DALY) SCDO:0000388 Sudden calamitous events producing great material damage, loss, and distress. They are the result of natural phenomena such as earthquakes, floods, etc. Calamities producing great damage, loss of life, and distress. They include results of natural phenomena and man-made phenomena. Normal conditions of existence are disrupted and the level of impact exceeds the capacity of the hazard-affected community. http://purl.bioontology.org/ontology/MESH/D004190 Sufficient SCDO:0000388 MESH:D004190 Disasters Natural Disaster Natural Disasters Disaster SCDO:0000391 A factor that modifies one or more aspects of a disease, such as sickle cell disease (SCD) (e.g. aspects such as temporal pattern, age of onset and mortality), for specific phenotype(s) of the disease. Request inclusion into relevant ontology These article contains a recent description of disease modifiers for SCD: http://www.nejm.org/doi/10.1056/NEJMra1510865 -- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4562292/ -- -- Paper mentioning haplotypes and severity: -- https://www.nature.com/scitable/topicpage/sickle-cell-anemia-a-look-at-global-8756219 -- -- Initially, the HP term "Clinical Modifier" (HP:0012823) was used to define this class, but its usage was found to be more "ontology-based" than what the SCDO intended. None SCDO (Jade Hotchkiss) Phenotypic Modifier Disease Modifier SCDO:0000396 A diagnostic ultrasound-based imaging technique operating at the frequency range of 2 megahertz. This machine makes use of the doppler effect to measure and visualise blood flow for possible pathology or lesions within blood vessels. Request inclusion into relevant ontology None SCDO (Clair Ingram) Doppler Ultrasound Machine - 2 Megahertz SCDO:0000397 An adverse event that has an outcome of a decreased amount of the drug excreted by the body. http://purl.obolibrary.org/obo/OAE_0000887 Sufficient SCDO:0000397 OAE:0000887 Drug Clearance Decreased AE SCDO:0000398 An adverse drug event that results in the development of a dependence on the drug. http://purl.obolibrary.org/obo/OAE_0000888 Sufficient SCDO:0000398 OAE:0000888 Drug Dependence AE SCDO:0000399 The amount of drug substances taken into the body. This seemed an obvious addition to the modifier class? None SCDO (Jade Hotchkiss) Drug Intake SCDO:0000400 A drug AE that has an outcome of lower threshold to the normal pharmacologic action of a drug. http://purl.obolibrary.org/obo/OAE_0000891 Sufficient SCDO:0000400 OAE:0000891 Drug Intolerance AE SCDO:0000401 An adverse event that results in symptoms that occur after the discontinuation of the use of a certain drug. http://purl.obolibrary.org/obo/OAE_0000893 Sufficient SCDO:0000401 OAE:0000893 Drug Withdrawal Syndrome AE SCDO:0000402 A neuropathy AE that is induced by a drug administration. http://purl.obolibrary.org/obo/OAE_0000165 Sufficient SCDO:0000402 OAE:0000165 Drug-Induced Neuropathy AE SCDO:0000405 'The combined specialties of diseases of the ear, pharynx, and larynx, including the upper respiratory tract and diseases of the head and neck, tracheobronchial tree, and esophagus. [Curator team: []]' http://medical-dictionary.thefreedictionary.com/ear+nose+and+throat Otolaryngology deprecated Ear, Nose and Throat true SCDO:0000407 A small hemorrhagic spot, larger than a petechia, in the skin or mucous membrane forming a nonelevated, rounded or irregular, blue or purplish patch. Suggest update to description. The term in the HPO was not detailed enough. Suggest update to description HP:0031364 Ecchymoses Ecchymosis SCDO:0000409 A physiological assay that uses standard ultrasound techniques to take two-dimensional pictures of the cardiovascular system and can produce accurate assessment of the velocity of blood and cardiac tissue at any arbitrary point using pulsed or continuous wave Doppler ultrasound. http://purl.obolibrary.org/obo/ERO_0000385 Sufficient SCDO:0000409 ERO:0000385 Cardiac ECHO Cardiac US Scan Diagnostic Ultrasound of Heart Echocardiographic procedure Echocardiography US Scan of Heart Ultrasonic cardiography Ultrasonography of Heart Ultrasound of Heart Echocardiogram SCDO:0000410 A machine used for ultrasonic recording of the size, motion, and composition of the heart and surrounding tissues. Request inclusion into relevant ontology. http://purl.bioontology.org/ontology/MESH/D004452 None SCDO (Jade Hotchkiss) Echocardiography Machine SCDO:0000414 Acquisition of knowledge as a result of instruction in a formal course of study. http://purl.bioontology.org/ontology/MESH/D004493 Sufficient SCDO:0000414 MESH:D004493 Schooling Education SCDO:0000415 The visual output that an electrocardiograph produces. Suggest update to description in ERO? http://en.wiktionary.org/wiki/electrocardiogram Suggest update to description ERO:0000383 ECG EKG Electrocardiogram SCDO:0000416 Device which makes prolonged electrocardiographic recordings on a portable tape recorder (Holter-type system) or solid-state device (real-time system), while the patient undergoes normal daily activities; useful in the diagnosis and management of intermittent cardiac arrhythmias and transient myocardial ischemia. http://bioportal.bioontology.org/ontologies/CRISP/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FCSP%2F1393-7164 Sufficient SCDO:0000416 CRISP:1393-7164 Ambulatory Electrocardiographic Monitor Electrocardiocorder Electrocardiographic Monitor SCDO:0000417 Recording of the moment-to-moment electromotive forces of the heart as projected onto various sites on the body's surface, delineated as a scalar function of time. The recording is monitored by a tracing on slow moving chart paper or by observing it on a cardioscope, which is a cathode ray tube display. Request that MESH removes ECG, EKG and Elecrocardiogram as synonyms. Sufficient SCDO:0000417 MESH:D004562 Electrocardiography SCDO:0000418 A graphic record of the electrical activity of the brain as recorded by an electroencephalograph. Request inclusion into relevant ontology http://medical-dictionary.thefreedictionary.com/electroencephalogram Few but definitions not freely available Electroencephalogram SCDO:0000419 An instrument that measures electrical potentials on the scalp and generates a record of the electrical activity of the brain. Request inclusion into relevant ontology http://medical-dictionary.thefreedictionary.com/electroencephalograph Few but definitions not freely available Encephalograph Electroencephalograph SCDO:0000420 Recording of electric currents developed in the brain by means of electrodes applied to the scalp, to the surface of the brain, or placed within the substance of the brain. http://purl.bioontology.org/ontology/MESH/D004569 Sufficient SCDO:0000420 MESH:D004569 EEG Electroencephalography SCDO:0000423 Media that facilitate transportability of pertinent information concerning patient's illness across varied providers and geographic locations. Some versions include direct linkages to online consumer health information that is relevant to the health conditions and treatments related to a specific patient. http://purl.bioontology.org/ontology/MESH/D057286 Sufficient SCDO:0000423 MESH:D057286 Computerized Health Records Computerized Medical Records Electronic Health Record Electronic Medical Record Electronic Medical Records Electronic Health Records SCDO:0000424 An electrochemical process in which macromolecules or colloidal particles with a net electric charge migrate in a solution under the influence of an electric current. Perhaps change label to "Hemoglobin Electrophoresis"? Exactsynonym "Hb ELP". See dc:source provided. http://purl.bioontology.org/ontology/MESH/D004586 Sufficient SCDO:0000424 MESH:D004586 Electrophoresis SCDO:0000431 The system pertaining to the stomach, intestines, and associated organs including liver, gallbladder, and pancreas. http://medical-dictionary.thefreedictionary.com/gastroenterology Gastroenterology deprecated Endocrine and Metabolic true SCDO:0000435 An environmental factor that modifies one or more aspects of sickle cell disease (SCD) (such as temporal pattern, age of onset and mortality) for specific phenotype(s) in the Phenotype class. Request inclusion into relevant ontology Perhaps include MESH term "Life Change Events" as a main sub-class, with "Disaster" (under Physical Environment) copied below it? None SCDO (Jade Hotchkiss) Environmental Disease Modifier SCDO:0000436 A method used to measure the relative activity of a specific enzyme or its concentration in solution. Typically an enzyme substrate is added to a buffer solution containing enzyme and the rate of conversion of substrate to product is measured under controlled conditions. Many classical enzymatic assay methods involve the use of synthetic colorimetric substrates and measuring the reaction rates using a spectrophotometer. http://purl.bioontology.org/ontology/MESH/D057075 Sufficient SCDO:0000436 MESH:D057075 Enzyme Assay Enzymatic Assay SCDO:0000437 Studies designed to examine associations, commonly, hypothesized causal relations. They are usually concerned with identifying or measuring the effects of risk factors or exposures. The common types of analytic study are case-control studies; cohort studies; and cross-sectional studies. Term to be adapted as necessary to match EDDA Study Designs Taxonomy http://purl.bioontology.org/ontology/MESH/D016021 Sufficient SCDO:0000437 MESH:D016021 Epidemiological Studies Epidemiologic Studies SCDO:0000438 Types and formulations of studies used in epidemiological and clinical research. Term to be adapted as necessary to match EDDA Study Designs Taxonomy http://purl.bioontology.org/ontology/MESH/D016020 MESH:D016020 Epidemiologic Study Characteristics deprecated Epidemiologic Study Characteristics as Topic true SCDO:0000440 A questionnaire to assess epilepsy, a condition characterized by recurrent seizures and which is a component of over 40 neurological disorders (Aminoff, et al., 2005). Sufficient SCDO:0000440 phenX:130401 Epilepsy Screener SCDO:0000441 The GHQ is a screening device for identifying minor psychiatric disorders in the general population and within community or non-psychiatric clinical settings such as primary care or general medical outpatients. Suitable for all ages from adolescent upwards (not children), it assesses the respondent's current state and asks if that differs from his or her usual state. It is therefore sensitive to short-term psychiatric disorders but not to long-standing attributes of the respondent. The self-administered questionnaire focuses on two major areas: inability to carry out normal functions; appearance of new and distressing phenomena. It is available in the following versions: GHQ-60 -- the fully detailed 60-item questionnaire; GHQ-30 -- a short form without items relating to physical illness; GHQ-28 -- a 28 item scaled version -- assesses somatic symptoms, anxiety and insomnia, social dysfunction and severe depression; GHQ-12 -- quick, reliable and sensitive short form, ideal for research studies. Add the different versions of this questionnaire, as listed in the description here. Request inclusion into NCIT below "Research or Clinical Assessment Tool". Goldberg, David; Hillier, Valerie (1979). "A scaled version of the General Health Questionnaire". Psychological Medicine. Cambridge University Press. 9 (01): 139–145. Few but definitions not freely available SCDO GHQ General Health Questionnaire (GHQ) SCDO:0000442 The GAD-7 is a self-administered patient questionnaire used as a screening tool and severity measure for generalised anxiety disorder. The GAD-7 score is calculated by assigning scores of 0, 1, 2, and 3, to the response categories of 'not at all', 'several days', 'more than half the days', and 'nearly every day', respectively, and adding together the scores for the seven questions. Scores of 5, 10, and 15 are taken as the cut-off points for mild, moderate and severe anxiety, respectively. When used as a screening tool, further evaluation is recommended when the score is 10 or greater. Spitzer RL, Kroenke K, Williams JB, et al; A brief measure for assessing generalized anxiety disorder: the GAD-7. Archives of Internal Medicine. 2006;166(10):1092-7. Few but definitions not specific enough NCIT:C88893 GAD-7 Generalised Anxiety Disorder Questionnaire Generalised Anxiety Disorder Questionnaire (GAD-7) SCDO:0000443 An educational process that provides information and advice to individuals or families about a genetic condition that may affect them. The purpose is to help individuals make informed decisions about marriage, reproduction, and other health management issues based on information about the genetic disease, the available diagnostic tests, and management programs. Psychosocial support is usually offered. http://purl.bioontology.org/ontology/MESH/D005817 Sufficient SCDO:0000443 MESH:D005817 Prenatal Genetic Counseling Genetic Counseling SCDO:0000444 A biological disease modifier that is of a genetic nature. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) Genetic Disease Modifier SCDO:0000447 Organized services to provide diagnosis, treatment, and prevention of genetic disorders. http://purl.bioontology.org/ontology/MESH/D033142 Sufficiient MESH:D033142 Genetic Services Genetic Service SCDO:0000448 Chromosomal, biochemical, intracellular, and other methods used in the study of genetics. This and its sub-classes need work! http://purl.bioontology.org/ontology/MESH/D005821 Sufficient SCDO:0000448 MESH:D005821 Genetic Technic Genetic Technics Genetic Techniques Genetic Technique SCDO:0000454 Elevated ocular pressure caused by clogging of the trabecular meshwork and by impaired aqueous humor outflow from blood in the anterior chamber (due to ocular trauma or surgery). Request inclusion into relevant ontology as more specific type (sub-class) of glaucoma. Ballas et al 2010 Am J Hematol None Glaucomas Glaucoma (Secondary to Presence of Blood in the Anterior Chamber of the Eye) SCDO:0000455 A test to assess the respondent's overall mental capability. Sufficient SCDO:0000455 phenX:130700 Global Mental Status Screener SCDO:0000456 A genetic locus responsible for the encoding of globins. Request inclusion into relevant ontology, perhaps below "Genetic Locus" in MESH. None SCDO (Jade Hotchkiss) Globin Locus SCDO:0000457 Measurement of the flow rate of filtered fluid through the kidney, calculated either by comparative measurements of substances in the blood and urine, or estimated from a blood test. http://www.ebi.ac.uk/efo/EFO_0005208 Sufficient SCDO:0000457 EFO:0005208 GFR Glomerular Filtration Rate SCDO:0000462 This gene encodes glucose-6-phosphate dehydrogenase. This protein is a cytosolic enzyme encoded by a housekeeping X-linked gene whose main function is to produce NADPH, a key electron donor in the defense against oxidizing agents and in reductive biosynthetic reactions. G6PD is remarkable for its genetic diversity. Many variants of G6PD, mostly produced from missense mutations, have been described with wide ranging levels of enzyme activity and associated clinical symptoms. G6PD deficiency may cause neonatal jaundice, acute hemolysis, or severe chronic non-spherocytic hemolytic anemia. Two transcript variants encoding different isoforms have been found for this gene. Exists in other ontologies but we have provided a description more relevant to its relationship with SCD. http://www.ncbi.nlm.nih.gov/gene/2539 Not relevant to context of sickle cell G-6-PD G6PD1 Glucose-6-Phosphate 1-Dehydrogenase Gene Glucose-6-Phosphate Dehydrogenase Gene G6PD SCDO:0000465 A deficiency or slowing down of growth pre- and postnatally greater than two standard deviations from the age- and sex-related normal. Suggest update to description in HPO. http://purl.obolibrary.org/obo/HP_0001510 Suggest update to description HP:0001510 Delayed Growth Growth Deficiency Growth Failure Growth Retardation Poor Growth Retarded Growth Growth Delay SCDO:0000466 A bioassay to measure haptoglobin, which is produced by the liver and transports hemoglobin to the liver for recycling. Suggest update to label in PhenX (from "Haptoglobin Level"). Suggest update to label phenX:10801 Haptoglobin Blood Test SCDO:0000487 Individual lifestyle and behavior which may or may not enhance or maintain good health. Suggest the NCIT updates their description for this term to include negative /risk inreasing behaviour? Include: -- gaining better control of your diabetes -- lowering cholesterol -- lowering blood pressure -- maintaining a healthy body weight -- eating a balanced diet -- Include these from MESH: -- Treatment Refusal -- Vaccination Refusal Sufficient SCDO:0000487 APAONTO:Health_Behavior Health Behavior Health Behaviour SCDO:0000488 People's beliefs about health problems, perceived benefits of action and barriers to action, and self-efficacy. Not relevant to context of sickle cell Health-Belief Model The health belief model suggests that health beliefs explain engagement (or lack of engagement) in health-promoting behaviour. Health Beliefs SCDO:0000489 Health financing is concerned with how financial resources are generated, allocated and used in health systems. Health financing policy focuses on how to move closer to universal coverage with issues related to: (i) how and from where to raise sufficient funds for health; (ii) how to overcome financial barriers that exclude many poor from accessing health services; or (iii) how to provide an equitable and efficient mix of health services. Request inclusion into relevant ontology None Health Care Resources Healthcare Resources Health Financing SCDO:0000490 Whether the respondent is covered by health insurance or some other form of health care coverage at the time of the interview. Suggest inclusion into MESH. The phenX term is actually referring to a protocol for collecting data on Health Insurance Coverage. The protocol is somewhat U.S. specific. Should probably be modified to be more relevant to the African setting. PhenX protocol: Health Insurance Coverage #11502 Negligable Also applicable to a population not just to an individual. Health Insurance Coverage SCDO:0000491 Degree to which individuals have the capacity to obtain, process and understand basic health information and services needed to make appropriate health decisions. http://purl.bioontology.org/ontology/MESH/D057220 Sufficient SCDO:0000491 MESH:D057220 Knowledge about Sickle Cell Disease Genetic Counseling Health Literacy SCDO:0000492 Health data accessible to the patient and others. http://purl.bioontology.org/ontology/MESH/D055991 Sufficient SCDO:0000492 MESH:D055991 Health Records, Personal Personal Health Information Personal Health Record Personal Health Records Personal Medical Record Personal Medical Records Health Records SCDO:0000493 The measure of the population's use of the health care services available to them. This includes the utilization of hospital resources, Personal Care Home (PCH) resources, and physician resources. Health care utilization and health status are used to examine how efficiently a health care system produces health in a population. Few but definitions not specific enough Health Care Service Utilization Health Care Utitlization Healthcare Utitlization Health Service Utilization SCDO:0000494 A system responsible for delivering services that improve, maintain or restore the health of individuals and their communities. This includes the care provided by hospitals and family doctors, but also less visible tasks such as the prevention and control of communicable disease, health promotion, health workforce planning and improving the social, economic or environmental conditions in which people live. Suggest update to description in Medline Plus Health Topics http://www.euro.who.int/en/health-topics/Health-systems/pages/health-systems Suggest update to description Health Care Delivery Health Care System Health Care Systems Health System SCDO:0000495 Utility measures of health related quality of life are preference values that patients attach to their overall health status. In clinical trials, utility measures summarize both positive and negative effects of an intervention into one value between 0 (equal to death) and 1 (equal to perfect health). These measures allow for comparison of patient outcomes of different diseases, and for comparison between various health care interventions. There are 2 different approaches to utility measurement. Request inclusion into relevant ontology http://www.ncbi.nlm.nih.gov/pubmed/7674256 None Health Utility Index Health Utility Measure Health Utility SCDO:0000496 The ease with which an individual can obtain needed medical services. Additional WG note: organization of health system [insurance]; electronic (portable) health records; special issues related to pain and pain medications; levels of care (primary, secondary, tertiary) (Location – [rural/urban; mobile units]; hours; affordability; timeliness). Availability of personnel. Equipment treatments other resources Negligable SCDO Access to Healthcare Health Care Access The WHO Constitution envisages "...the highest attainable standard of health as a fundamental right of every human being." The right to health includes access to timely, acceptable, and affordable health care of appropriate quality. Healthcare Access SCDO:0000497 Dietary patterns which have been found to be important in reducing disease risk. http://purl.bioontology.org/ontology/MESH/D000072001 Sufficient SCDO:0000497 MESH:D000072001 Healthy Eating Healthy Diet SCDO:0000498 A pattern of behavior involving lifestyle choices which ensure optimum health. Examples are eating right; maintaining physical, emotional, and spiritual wellness, and taking preemptive steps against communicable diseases. http://purl.bioontology.org/ontology/MESH/D000070497 Sufficient SCDO:0000498 MESH:D000070497 Healthy Life Style Healthy Lifestyle SCDO:0000500 Examinations used to diagnose and treat heart conditions. http://purl.bioontology.org/ontology/MESH/D006334 Sufficient SCDO:0000500 MESH:D006334 Heart Function Tests Pulmonary Function Test Heart Function Test SCDO:0000501 The number of times the heart ventricles contract per unit of time, usually per minute. http://www.ebi.ac.uk/efo/EFO_0004326 Sufficient SCDO:0000501 EFO:0004326 Heart Beat Pulse Pulse Rate Heart Rate SCDO:0000502 Any value resulting from the quantification of a morphological or physiological parameter pertaining to the heart valves. Request inclusion into relevant ontology. Perhaps below "Heart Measurement" in the CMO. Can add sub-classes as per the measurements given in the Diagnostic Criteria below the Protocol section in PhenX for "Heart Valve Function". Sub-classes that are also morphological measurements can be included below "Body Morphological Measurement" None SCDO (Jade Hotchkiss) Heart Valve Measurement SCDO:0000504 A measurement device used to perform complete blood counts, erythrocyte sedimentation rates (ESRs), or coagulation tests. http://purl.obolibrary.org/obo/ERO_0000494 Sufficient SCDO:0000504 ERO:0000494 Haematology Analyser Hematology Analyzer SCDO:0000505 A test to detect potential blood disorders or diseases in people who do not have any symptoms of disease. Request inclusion into relevant ontology. Few but definitions not freely available Haematology Screening Test Hematology Screening Test SCDO:0000506 Transfer of hematopoietic stem cells from bone marrow or blood between individuals within the same species (transplantation, homologous) or transfer within the same individual (transplantation, autologous). Hematopoietic stem cell transplantation has been used as an alternative to bone marrow transplantation in the treatment of a variety of neoplasms. http://purl.bioontology.org/ontology/MESH/D018380 Sufficient SCDO:0000506 MESH:D018380 BMT Bone Marrow Transplant Hematopoietic SCT Hematopoietic Stem Cell Transplantation SCDO:0000507 The blood-making organs and tissues, principally the bone marrow and lymph nodes. http://purl.bioontology.org/ontology/MESH/D006413 MESH:D006413 deprecated Hematopoietic System true SCDO:0000508 Presence of blood in the urine. http://purl.bioontology.org/ontology/MESH/D006417 Sufficient SCDO:0000508 MESH:D006417 Blood in Urine Hematurias Hematuria SCDO:0000510 This gene encodes the enzyme, heme oxygenase 1, an essential enzyme in heme catabolism and cellular homeostasis. Suggest update to description in NCIT (for "HMOX1 Gene") http://www.ncbi.nlm.nih.gov/gene/3162 Suggest update to description HMOX1 Gene HO-1 HO1 Gene Heat Shock Protein, 32-kD Gene Heme Oxygenase (Decycling) 1 Gene Heme Oxygenase 1 gene Hemeoxygenase 1 Gene Hemoxygenase-1 Gene HMOX1 SCDO:0000511 Organs involved in the production of BLOOD, including the cellular and the molecular components essential in providing defense against foreign organisms or substances. obsolete Hemic and Immune Systems true SCDO:0000513 A commonly occurring abnormal hemoglobin in which lysine replaces a glutamic acid residue at the sixth position of the beta chains. It results in reduced plasticity of erythrocytes. http://purl.bioontology.org/ontology/MESH/D006444 Sufficient SCDO:0000513 MESH:D006444 Hb C HbC HbC Hemoglobin Hemoglobin C SCDO:0000514 An abnormal hemoglobin resulting from the substitution of valine for glutamic acid at position 6 of the beta chain of the globin moiety. The heterozygous state results in sickle cell trait, the homozygous in sickle cell anemia. http://purl.bioontology.org/ontology/MESH/D006451 Sufficient SCDO:0000514 MESH:D006451 Haemoglobin S Hb S HbS HbS Haemoglobin HbS Hemoglobin Sickle Haemoglobin Sickle Hemoglobin Hemoglobin S SCDO:0000515 An abnormal hemoglobin composed of four beta chains. It is caused by the reduced synthesis of the alpha chain. This abnormality results in alpha-thalassemia. http://purl.bioontology.org/ontology/MESH/D006447 Sufficient SCDO:0000515 MESH:D006447 Hb H HbH HbH Hemoglobin Hemoglobin H SCDO:0000516 None deprecated Hemoglobin A2 Profile true SCDO:0000517 An abnormal hemoglobin, composed of four gamma globin chains, causing it to have an extremely high affinity for oxygen, resulting in almost no oxygen delivery to the tissues. Additional info from the definition in HPO: "Hb Barts (Hemoglobin Barts) is a tetramer with four gamma globin chains, and is essentially pathognomonic for one or another form of alpha thalassemia. Hb Barts has an extremely high affinity for oxygen, resulting in almost no oxygen delivery to the tissues." Suggest update to description in HP as we have done. http://purl.obolibrary.org/obo/HP_0005507 Suggest update to description HP:0005507 Haemoglobin Bart's Haemoglobin Barts Hb Bart's Hb Barts Hemoglobin Bart's Hemoglobin Barts SCDO:0000518 The most severe form of alpha-thalassemia and is almost always lethal, and characterized by fetal onset of generalized edema, pleural and pericardial effusions, and severe hypochromic anemia. It is caused by the presence of Hemoglobin Barts, a hemoglobin with four gamma chains, which has an extremely high affinity for oxygen, resulting in almost no oxygen delivery to the tissues Suggest update to description in ORDO as we have done. http://www.orpha.net/ORDO/Orphanet_163596 Suggest update to description Orphanet:163596 Alpha-Thalassemia Hydrops Fetalis Alpha-Thalassemia Major Haemoglobin Barts Hydrops Fetalis Hb Barts Hb Barts Syndrome Hemoglobin Bart's Hydrops Fetalis Hemoglobin Barts Hydrops Fetalis Syndrome Homozygous Alpha 0-Thalassemia Hemoglobin Barts Hydrops Fetalis SCDO:0000519 An autosomal recessive disorder resulting from the production of hemoglobin C, secondary to an amino acid substitution of lysine for glutamic acid in the sixth position of the beta chain (E6K), and characterized by mild hemolytic anemia and occasionally jaundice, though most patients are asymptomatic. Suggest update to description in NCIT http://newbornscreeningcodes.nlm.nih.gov/nb/sc/condition/Hb-F-C Suggest update to description NCIT:C34675 Haemoglobin C Disease Hb C-Disease Hemoglobin C Disease SCDO:0000520 The inheritance of the gene for hemoglobin C from one parent and a gene for normal adult hemoglobin (hemoglobin A) from the other parent. Request inclusion into NCIT below "Hemoglobin Trait". http://www.sickle-thal.nwlh.nhs.uk/blood/haemoglobinc.aspx Few but definitions not freely available Haemoglobin C-A Disorder Hb AC Hemoglobin C-A Disorder Heterozygous for Hb C Hemoglobin C Trait SCDO:0000521 'A form of beta-thalassemia with a phenotype of mild to moderate hemolytic anemia. Patients are often asymptomatic but if present symptoms include anemia and enlarged spleen.' The description could be more detailed. http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=GB&Expert=231242 Hb C-Beta Thalassemia Syndrome Hemoglobin C Beta-Thalassemia deprecated Hemoglobin C-Beta Thalassemia true SCDO:0000522 A test to measure the presence and amount of a variant of hemoglobin in the blood. Many terms below "Hemoglobin Variant Test" in SNOMED CT could be added. Suggest update to label and description in NCIT (from "Hemoglobin Variant Measurement" and "A test to measure the variants of hemoglobin.") It is not clear whether this term was is in fact a synonym of "Hemoglobin Profile Assay". We assumed it wasn't. If it actually is, we need to address the ambiguity caused. http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C103845 Suggest update to label and description NCIT:C103845 Haemoglobin Variant Observation Haemoglobin Variant Test Haemoglobinopathy Screen Hemoglobin Variant Measurement Hemoglobin Variant Observation Hemoglobinopathy Screen Hemoglobin Variant Test SCDO:0000524 An autosomal recessive hemoglobinopathy characterized by production of abnormal variant hemoglobin known as hemoglobin D, with no or mild clinical manifestations (splenomegaly, very mild anemia). Suggest update to description in ORDO http://www.doh.wa.gov/Portals/1/Documents/5220/HbDFactSheet.pdf Suggest update to description DOID:5378 Hb DD Homozygous Hemoglobin D Hemoglobin D Disease SCDO:0000525 The inheritance of the gene for hemoglobin D from one parent and a gene for normal adult hemoglobin (hemoglobin A) from the other parent. Request inclusion into NCIT below "Hemoglobin Trait". http://www.doh.wa.gov/Portals/1/Documents/5220/HbDFactSheet.pdf Few but definitions not freely available SCDO (Jade Hotchkiss) Hb AD Hemoglobin D Trait SCDO:0000526 'Hemoglobin D/xcexb2xc2xb0 thalassemia is a form of beta-thalassemia which results in a mild to moderate clinical picture. The severity of the condition depends on the degree of thalassemia and how it affects production of Hemoglobin A, however this condition is often considered fairly benign.' http://www.doh.wa.gov/Portals/1/Documents/5220/HbDFactSheet.pdf HbD - BT Hemoglobin D Beta-Thalassemia deprecated Hemoglobin D-Beta Thalassemia true SCDO:0000527 An unusual hemoglobin that shows all the electrophoretic features of Hb D, but has no inherited disability. This hemoglobin has a beta 87 Thr > Lys mutation. Request inclusion into NCIT below "Hemoglobin"/"Hemoglobin Variant"/"Unusual Hemoglobin". Few but definitions not freely available Hemoglobin D (badan) Hemoglobin D-Ibadan SCDO:0000528 An abnormal hemoglobin (one of the types of hemoglobin D) in which glutamine replaces glutamic acid at codon 121 of beta globin. Request inclusion in the HPO, below "Abnormal Hemoglobin"/"Hemoglobin D". http://health.utah.gov/nsp/Disorders/HB/Hb_D_Disease_DD/FactSheet_Provider_HbDD_En.pdf Few but definitions not freely available Haemoglobin D-Punjab Hb D-Los Angelese Hb D-Punjab Hemoglobin D (Chicago) Hemoglobin D (Los Angeles) Hemoglobin D (North Carolina) Hemoglobin D (Portugal) Hemoglobin D (Punjab) Hemoglobin Oak Ridge Hemoglobin D-Punjab SCDO:0000529 A disease caused by atypical hemoglobins molecules other than hemoglobin C,D,E, F, H, O-Arab and S. adapted from description under ID SCDO:0001065 SCDO:0001065 http://newbornscreeningcodes.nlm.nih.gov/nb/sc/condition/Hb-F-and-other-than-A-C-D-E-F-H-O-Arab-S deprecated Hemoglobin Disease Other than C,D,E,F,H,O-Arab,S true SCDO:0000530 An autosomal recessive haemoglobinopathy characterized by an abnormal form of haemoglobin called haemoglobin E, which disrupts the oxygen-carrying ability of red blood cells. The condition can lead to mild or moderate hemolytic anemia; however, this condition often has no clinical manifestations. with a generally benign, asymptomatic presentation. http://newbornscreeningcodes.nlm.nih.gov/nb/sc/condition/Hb-F-E Sufficient SCDO:0000530 ORPHA:2133 Haemoglobin E Disease Hb E-Disease Hemoglobin E Disease SCDO:0000531 The inheritance of the gene for hemoglobin E from one parent and a gene for normal adult hemoglobin (hemoglobin A) from the other parent. Request inclusion into NCIT below "Hemoglobin Trait". http://newbornscreeningcodes.nlm.nih.gov/nb/sc/condition/Hb-F-A-E Few but definitions not freely available SCDO Hb AE Hb E Trait Hb E-carriers generally do not have any signs or symptoms related to abnormal hemoglobin. Hemoglobin E Trait SCDO:0000532 'Hemoglobin E/xcexb2+ thalassemia is a form of beta-thalassemia that is often, but not always, milder than hemoglobin E/xcexb2xc2xb0 thalassemia. This condition shows a marked clinically diverse picture whereby abnormalities of xcexb2-globin chain synthesis result almost asymptomatic anemia to more severe transfusion-dependant anemia (Vichinsky, 2007).' http://www.orpha.net/consor/cgi-bin/Disease_Search.php?lng=EN&data_id=19177&Disease_Disease_Search_diseaseGroup=Hemoglobin-D-Beta-Thalassemia&Disease_Disease_Search_diseaseType=Pat&Disease(s)/group%20of%20diseases=Hemoglobin-E-beta-thalassemia-syndrome&title=Hemoglobin-E-beta-thalassemia-syndrome&search=Disease_Search_Simple Haemoglobin E-Beta Thalassemia Hemoglobin E Beta-Thalassemia deprecated Hemoglobin E-Beta Thalassemia true SCDO:0000533 The score of fetal hemoglobin (Hb F) in the blood of an individual. Description not clear enough. None SCDO (Gaston K Mazandu) deprecated Hemoglobin F Profile true SCDO:0000535 A variant of Hemoglobin Lepore Syndrome. http://en.wikipedia.org/wiki/Hemoglobin_Lepore_syndrome Hb Lepore Baltimore obsolete Hemoglobin Lepore Baltimore true SCDO:0000536 A variant of Hemoglobin Lepore Syndrome. Crossover occurs between glutamine at position 87 of delta chain and histidine at position 116 of beta chain. It is associated with unusual high levels of Hb F. This is the only one of the three variants of described in association with HbS. Request inclusion into relevant ontology http://en.wikipedia.org/wiki/Hemoglobin_Lepore_syndrome None Hb Lepore Boston Syndrome Hb Lepore Washington Syndrome Hb Lepore Washington-Boston Syndrome Hemoglobin Lepore Boston-Washington Hemoglobin Lepore Washington Syndrome Hemoglobin Lepore Washington-Boston Syndrome Hemoglobin Lepore Boston Disease SCDO:0000537 A variant of Hemoglobin Lepore Syndrome. http://en.wikipedia.org/wiki/Hemoglobin_Lepore_syndrome Hb Hollandia obsolete Hemoglobin Lepore Hollandia true SCDO:0000539 The inheritance of the gene for hemoglobin Lepore from one parent and a gene for normal adult hemoglobin (hemoglobin A) from the other parent. Request inclusion into relevant ontology http://en.wikipedia.org/wiki/Hemoglobin_Lepore_syndrome Few but definitions not freely available SCDO (Jade Hotchkiss) Heterozygous Hb Lepore Hemoglobin Lepore Trait SCDO:0000540 'A form of beta-thalassemia in which the patient is compound heterozygous for hemoglobin lepore and beta-thalassemia, which results in beta-thalassemia intermedia to beta-thalassemia major. [Curator team: []]' Add HBD to Disease Modifiers (below Gene Product)? And link to it. Hb Lepore-B-Thalassaemia Hemoglobin Lepore-B-Thalassaemia Hemoglobin Lepore-Beta Thalassaemia Syndrome deprecated Hemoglobin Lepore-Beta Thalassaemia true SCDO:0000541 A type of dominant hereditary methemoglobinemia resulting from the production of hemoglobin M, which is readily oxidised to yield excess methemoglobin which leads to cyanosis. Suggest update to description in MESH http://medlineplus.gov/ency/article/000562.htm Few but definitions not available SCDO (Jade Hotchkiss) Autosomal Dominant Congenital Methemoglobinemia Type II Autosomal Dominant Hereditary Methemoglobinemia Type II Hereditary MetHb Type II Hereditary Methemoglobinemia Type II M Hemoglobinopathy Second Form of Inherited MetHb Hemoglobin M Disease SCDO:0000542 Hemoglobin M Disease is autosomal dominant, thus does not seem to have a "trait" condition. Requires definition and source. None obsolete - Hemoglobin M Trait true SCDO:0000544 A very rare autosomal recessive hemoglobinopathy characterized by an abnormal form of hemoglobin called hemoglobin O-Arab. It is associated with a mild to moderate anemia. Request inclusion into relevant ontology http://onlinelibrary.wiley.com/doi/10.1002/pbc.24414/pdf None Hb O-Arab Disease Homozygous Hb O-Arab Homozygous Hemoglobin O-Arab Hemoglobin O-Arab Disease SCDO:0000545 The inheritance of hemoglobin O-Arab from one parent and a gene for normal adult hemoglobin (hemoglobin A) from the other parent. Request inclusion into NCIT below "Hemoglobin Trait". http://onlinelibrary.wiley.com/doi/10.1002/pbc.24414/pdf Few but definitions not freely available Hb A/O-Arab Hb AO-Arab Heterozygous Hb O-Arab Heterozygous Hemoglobin O-Arab Hemoglobin O-Arab Trait SCDO:0000546 The type and relative amounts of various normal and abnormal hemoglobin types. Request inclusion into relevant ontology. http://labtestsonline.org/understanding/analytes/sickle/tab/test/ None SCDO Hemoglobin Profile SCDO:0000547 A bioassay that measures and identifies the different types of hemoglobin in the bloodstream. It can be used to identify and characterize the different variants in structure and synthesis of hemoglobin that cause sickle cell disease. PhenX protocol: Hemoglobin Characterization #830301 Sufficient SCDO:0000547 phenX:830301 Haemoglobin Characterization Haemoglobinopathy Screen Hb Electrophoresis Plus Solubility Hemoglobin Characterization Hemoglobin Electrophoresis Hemoglobin Electrophoresis plus Solubility Hemoglobin Fractionation Hemoglobinopathy Evaluation Hemoglobinopathy Evaluation Profile Blood Test Hemoglobinopathy Fractionation Profile Blood Test Hemoglobinopathy Screen Hemoglobin Profile Assay SCDO:0000548 A test to quantify the presence of hemoglobin S in the blood and therefore determine whether a person has sickle cell trait or sickle cell disease. In SNOMED CT this term is "Sickle cell identification". Request inclusion into relevant ontology. http://www.questdiagnostics.com/testcenter/TestDetail.action?ntc=31852 Few but definitions not freely available SCDO (Clair Ingram) Hemoglobin S Measurement Sickle Cell Identification Hemoglobin S Test SCDO:0000551 The inheritance of one of the faulty genes that causes thalassemia. Request inclusion into relevant ontology Few but definitions not freely available SCDO (Jade Hotchkiss) Thalassemia Trait SCDO:0000552 An inherited disorder of the structure and/or synthesis of hemoglobin, with a variable phenotype expression ranging from benign to severe. Suggest update to description in NCIT Suggest update to description NCIT:C3092 Hemoglobinopathy SCDO:0000553 Hemoglobinopathy Toms River, is also known as transient neonatal cyanosis and anemia due to toms river hemoglobin. An important gene associated with Hemoglobinopathy Toms River is HBG2 (Hemoglobin Subunit Gamma 2. Anemia due to Toms River Hemoglobin Transient Neonatal Cyanosis obsolete Hemoglobinopathy Toms River true SCDO:0000556 The distance between the lower border of the liver in the mid-clavicular line, and the upper border of the liver in the mid-clavicular line. The description needs to be reviewed by an expert. Request inclusion into Clinical Measurement Ontology, below "liver size measurement". http://en.wikipedia.org/wiki/Liver_span None Liver Span Hepatic Span SCDO:0000557 A test for Hepatitis B Virus. Which Hepatitis B Test is to be referred to here? (There are various different types below "Immunology Test" in the "Sage Bionetworks Synapse Ontology") HBV Test Hepatitis B Virus Test obsolete Hepatitis B Test true SCDO:0000558 A test for Hepatitis C Virus. Is this test for viral load measurement or or antibody measurement? (See terms below "Immunology Test" in the "Sage Bionetworks Synapse Ontology") obsolete Hepatitis C Test true SCDO:0000559 A rare red cell disorder classified principally into two clinical phenotypes: autosomal recessive congenital (or hereditary) methemoglobinemia types I and II (RCM/RHM type 1; RCM/RHM type 2). http://www.orpha.net/consor/cgi-bin/Disease_Search.php?lng=EN&data_id=3290&disease=Hereditary-methemoglobinemia&search=Disease_Search_Simple Sufficient SCDO:0000559 ORPHA:621 Congenital Methemoglobinemia HM Hereditary MetHb Hereditary Methemoglobinemia SCDO:0000564 Replacement of the hip joint. http://purl.bioontology.org/ontology/MESH/D019644 Sufficient SCDO:0000564 MESH:D019644 Hip Prosthesis Implantation Hip Replacement Arthroplasty Hip Replacements, Total Replacement Arthroplasties, Hip Total Hip Replacement Hip Replacement Arthroplasty SCDO:0000565 A study that compares a group of participants receiving an intervention with a similar group from the past who did not. http://purl.bioontology.org/ontology/MESH/D065386 Sufficient SCDO:0000565 MESH:D065386 Historically Controlled Study SCDO:0000566 A questionnaire to determine whether an individual has had a traumatic brain injury (TBI). Suggest update to label as we have done. We are using "History of Head Trauma" below Personal Attribute. PhenX protocol: History of Head Trauma #130601 Suggest update to label phenX:130600 History of Head Trauma Questionnaire History of Head Trauma Diagnostic Instrument SCDO:0000567 A questionnaire to determine if the respondent has a history of kidney failure. Link to? -- Kidney Failure -- Personal Attribute---> Personal medical history --> History of Kidney Failure Suggest update to label as we have done. We are using "History of Kidney Failure" below Personal Attribute. PhenX protocol: Personal History of Kidney Failure #140601 Suggest update to label phenX:140600 History of Kidney Failure Questionnaire History of Kidney Failure Diagnostic Instrument SCDO:0000568 A questionnaire to determine if the respondent has had an ischemic infarction (i.e. stroke) and/or any symptoms related to this event. Suggest update to label as we have done. We are using "History of Stroke" below Personal Attribute. PhenX protocol: History of Stroke - Ischemic Infarction and Hemorrhage #130301 Suggest update to label phenX:130300 History of Stroke - Ischemic Infarction and Hemorrhage - Questionnaire History of Stroke - Ischemic Infarction and Hemorrhage - Diagnostic Instrument SCDO:0000570 A questionnaire to determine a respondent's history of type 1 or type 2 diabetes. Link to? -- Personal Attribute---> Personal medical history --> History of Type I and Type 2 Diabetes Suggest update to label as we have done. We are using "History of Type I and Type 2 Diabetes" below Personal Attribute. PhenX protocol: Personal History of Type 1 and Type 2 Diabetes #140501 Suggest update to label phenX:140500 History of Type I and Type 2 Diabetes Diagnostic Instrument SCDO:0000571 A bioassay to measure human immunodeficiency virus (HIV) antibodies and/or HIV antigens in order to determine whether an individual has an HIV infection. Also below "Immunochemical Assay"? Few but definitions not freely available HIV Assay Human Immunodeficiency Virus Assay Human Immunodeficiency Virus Test HIV Test SCDO:0000572 The HADS consists of 2 subscales each with 7 items for measuring anxiety, and 7 items for depression rated from 0 - 3. Anxiety and depression scores are obtained by adding up the ratings of the items on each subscale. A score above 8 in any of the subscales indicates that the patient has experienced clinically significant anxiety or depression over the past week. Zigmond A.S. and Snaith R.P. (1983). The hospital anxiety and depression scale. Acta Psychiatry Scandinavia, 67, 361-370. Anie, K.A.; Green, J.; Tata, P.; Fotopoulos, C. E.; Oni, L. and Davies, S. C. (2002) Self-help manual-assisted cognitive behavioural therapy for sickle cell disease. Behavioural and Cognitive Psychotherapies, 30, 451-458 multiple Patient Reported Outcome Clinic Patients Widely used around the world, also used in SCD Adults (18 to 91 years) Few but definitions not specific enough NCIT:C103520 HADS HADS Questionnaire HADS01 Hospital Anxiety and Depression Scale Hospital Anxiety and Depression Scale Questionnaire Hospital Anxiety and Depression Scale Questionnaire (HADS) Hospital Anxiety and Depression Scale (HADS) SCDO:0000573 The confinement of a patient in a hospital. Perhaps "Hospital Utilization" would be better here? http://purl.bioontology.org/ontology/MESH/D006760 Sufficient SCDO:0000573 MESH:D006760 Hospital Admission Hospitalisation Hospitalisations Hospitalizations Hospitalization SCDO:0000574 A record of those living in the respondent's household and about his or her relationship with them. Request inclusion into MESH below "Social Conditions"? PhenX protocol: Household Roster-Relationships #11402 Negligable phenX:11400 Household Roster-Relationships SCDO:0000576 A unique treatment that administers electrolyte-packed IV fluids directly into a patient's bloodstream. Depending on the patient's needs, the fluid may be enhanced with additives such as calcium, magnesium sulfate or a Vitamin B complex. It is a far more efficient method of absorption when compared to the traditional method of drinking liquids/electrolytes. Suggest update to description in NCIT (currently no description) Suggest update to description NCIT:C66896 Hydration Therapy SCDO:0000580 An antineoplastic agent that inhibits DNA synthesis through the inhibition of ribonucleoside diphosphate reductase. Sufficient SCDO:0000580 MESH:D006918 Hydrea Hydroxycarbamide Oncocarbide Hydroxyurea SCDO:0000581 A causal adverse drug event that is induced by hydroxyurea. Request inclusion into OAE below "Causal Adverse Drug Event". None SCDO (Jade Hotchkiss) Hydroxyurea-Induced Adverse Event SCDO:0000582 A hydroxyurea-induced adverse event that has an outcome relating to or affecting the skin. Request inclusion into OAE below "Hydroxyurea-Induced Adverse Event" (also suggested by us for inclusion). Or Obsolete and use an object property (has adverse events) to link Hydroxyea to Cutaneous. None SCDO (Jade Hotchkiss) Hydroxyurea-Induced Cutaneous Adverse Event SCDO:0000583 A hydroxyurea-induced adverse event that has the outcome of splenomegaly. Request inclusion into OAE below "Hydroxyurea-Induced Adverse Event" (also suggested by us for inclusion). Or Delete and use an object property (has adverse events) to link Hydroxyea to Splenomegaly. None SCDO (Jade Hotchkiss) Hydroxyurea-Induced Splenomegaly Adverse Event SCDO:0000588 Abnormally high potassium concentration in the blood, most often due to defective renal excretion. It is characterized clinically by electrocardiographic abnormalities (elevated T waves and depressed P waves, and eventually by atrial asystole). In severe cases, weakness and flaccid paralysis may occur. (Dorland, 27th ed). http://purl.bioontology.org/ontology/MESH/D006947 Sufficient SCDO:0000588 MESH:D006947 High Blood Potassium Levels Hyperkalemias Hyperpotassemia Hyperpotassemias Hyperkalemia SCDO:0000593 Excessive pigmentation of the skin, usually as a result of increased epidermal or dermal melanin pigmentation, hypermelanosis. Hyperpigmentation can be localized or generalized. The condition may arise from exposure to light, chemicals or other substances, or from a primary metabolic imbalance. Sufficient SCDO:0000593 MESH:D017495 Hypermelanoses Hypermelanosis Hyperpigmentation of the skin Skin Hyperpigmentation Hyperpigmentation SCDO:0000598 Drugs used to induce drowsiness or sleep or to reduce psychological excitement or anxiety. http://purl.bioontology.org/ontology/MESH/D006993 Sufficient SCDO:0000598 MESH:D006993 Hypnotics Sedatives Sedatives and Hypnotics Hypnotics and Sedatives SCDO:0000607 The ICD-10-CM diagnosis classification system developed by the Centers for Disease Control and Prevention for use in all U.S. health care treatment settings. Diagnosis coding under this system uses a different number of digits and some other changes, but the format is very much the same as ICD-9-CM. The National Center for Health Statistics (NCHS), the Federal agency responsible for use of the International Statistical Classification of Diseases and Related Health Problems, 10th revision (ICD-10) in the United States, has developed a clinical modification of the classification for morbidity purposes. The ICD-10 is used to code and classify mortality data from death certificates, having replaced ICD-9 for this purpose as of January 1, 1999. ICD-10-CM is the replacement for ICD-9-CM, volumes 1 and 2, effective October 1, 2015. Request inclusion into relevant ontology, perhaps below "Clinical Coding" in MESH. https://www.cdc.gov/nchs/icd/icd10cm.htm https://www.findacode.com/icd-10-cm/icd-10-cm-diagnosis-codes-set.html None ICD-10-CM Diagnosis Codes SCDO:0000611 The IPQ-R is an 84-item self-completed instrument developed to provide a quantitative measurement of the components of illness representations, as described by Leventhal's Common-Sense Model (CSM) of selfregulation it is divided into 3 sections: identity subscale (14 symptoms), causal subscale (18 causes), and a third section which contains 7 subscales, including consequences, timeline acute/chronic and cyclical, personal and treatment control/cure, illness coherence, and emotional representations. The questionnaire wording can be adapted to the specific illness by replacing the word illness with the name of the condition. For the identity subscale, respondents are asked if they have experienced a number of symptoms since their illness, and if they feel the symptoms are related to their current illness. Response is by circling 'yes' or 'no' to each question. Responses are then summed to give an overall score. For the causal subscale, respondents are asked what they perceive to be the cause of their illness and are asked to respond to each of the listed causes using a 5-point Likert style scale, ranging from strongly disagree to strongly agree. Respondents are also asked to rank the 3 most important factors believed to be the cause of their illness. The third section (7 subscales) is scored by summing responses to each item is on a 5-point Likert style scale, ranging from strongly disagree to strongly agree. All items for each of the subscales are summed to give an overall score. High scores on the identity, consequences, timeline acute/chronic and cyclical subscales represent strongly held beliefs about the number of symptoms attributed, the negative consequences, and the chronicity and cyclical nature of the illness. High scores on the personal and treatment control and coherence subscales represent positive beliefs about controllability and a personal understanding of the illness. Request inclusion into NCIT below "Research or Clinical Assessment Tool". Moss-Morris R, Weinman J, Petrie KJ, Horne R, Cameron LD, Buick D (2002). The Revised Illness Perception Questionnaire (IPQ-R). Psychol Health 17:1-16. multiple Patient Reported Outcome Clinic Patients many Good psychometric properties, widely used around the world, has been translated into several languages. Adults None Moss-Morris R, Weinman J, Petrie KJ, Horne R, Cameron LD, Buick D (2002). The Revised Illness Perception Questionnaire (IPQ-R). Psychol Health 17:1-16. IPQ-R Illness Perception Questionnaire Revised Illness Perception Questionnaire Revised (IPQ-R) SCDO:0000615 The body's defense mechanism against foreign organisms or substances and deviant native cells. It includes the humoral immune response and the cell-mediated response and consists of a complex of interrelated cellular, molecular, and genetic components. http://purl.bioontology.org/ontology/MESH/D007107 MESH:D007107 deprecated Immune System true SCDO:0000616 An assay that identifies a substance (especially a protein) by its action as an antigen. Request inclusion into relevant ontology None Immunochemical Assay SCDO:0000618 A drug adverse event that has an outcome of decreased levels of immunosuppressant drugs in the patient's body. http://purl.obolibrary.org/obo/OAE_0001071 Sufficient SCDO:0000618 OAE:0001071 Immunosuppressant Drug Level Decreased AE SCDO:0000619 An assay that employs immunoturbidimetry, a method that measures the absorbance of light from a sample which is used for quantifying an amount of analyte based on the level of turbidity produced by the formation and precipitation of an immune complex containing the analyte. Request inclusion into relevant ontology. NCIT contains "Immunoturbidimetry", but not "Immunoturbidimetry Assay". Do we rather want to have this term as "Immunoturbidimetry"? http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C106536 None Immunoturbidimetry Test Immunoturbidimetry Assay SCDO:0000643 Substances causing insects to turn away from them or reject them as food. http://purl.bioontology.org/ontology/MESH/D007302 Sufficient SCDO:0000643 MESH:D007302 Insect Repellents SCDO:0000649 A standardized tool designed to assess a child's development as compared to same-age peers. It has components that involve both direct observation and interaction with a child as well as caregiver questionnaires. It consists of five domains (cognitive, motor, language, social-emotional, and adaptive behavior). Life stage: Infant, Toddler, Child Suggest update to description in NCIT (we're not using their description, but their description says "from one to twenty-four months of age") The Sickle Cell Disease Neurology, Quality of Life, and Health Services Working Group recognizes that there is an age overlap between the Bayley-III and the Wechsler Preschool and Primary Scale of Intelligence-Fourth Edition (WPPSI - IV). The Working Group recommends that providers use their clinical judgment, consider the purpose of testing participants, and refer to the frequently asked questions section of the Pearson website for Bayley-III and the WPPSI-IV for guidance on selecting an age-appropriate test. http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820504 PhenX protocol: Intelligence Scale - Birth to 3.5 years #820504 Suggest update to description NCIT:C99150 Bayley Scale of Infant Development III Bayley Scales of Infant and Toddler Development, Third Edition Bayley Scales of Infant and Toddler Development, Third Edition (Bayley-III) Bayley-III Intelligence Scale - Birth to 3.5 years SCDO:0000650 An adverse drug event that results in the intentional use of a drug in the wrong way (recreationally etc). http://purl.obolibrary.org/obo/OAE_0001093 Sufficient SCDO:0000650 OAE:0001093 Intentional Drug Misuse AE SCDO:0000651 A study that uses observations at multiple time points before and after an intervention (the interruption), in an attempt to detect whether the intervention has had an effect significantly greater than any underlying trend over time. http://purl.bioontology.org/ontology/MESH/D065186 Sufficient SCDO:0000651 MESH:D065186 ITS Studies Interrupted Time Series Analysis SCDO:0000653 Intracerebral hemorrhage (ICH) is when blood suddenly bursts into brain tissue, causing damage to the brain. Should this term be merged with "Cerebral Hemorrhage" and "Intracerebral Haemorrhage" made a synonym of "Cerebral Hemorrhage"? -- -- Specify description source and source for additional info. Intracerebral Bleeding deprecated-Intracerebral Haemorrhage true SCDO:0000656 CSF pressure less than 6 cm of H2O in patients with clinical presentation compatible with intracranial hypotension, which are postural headache, nausea, vomiting, neck pain, visual and hearing disturbances, and vertigo. It most commonly results from CSF leaks somewhere along the neuraxis. Suggest update to description in DOID (currently no description) Spontaneous intracranial hypotension is typically encountered in middle age (30-50 years of age) and has a predilection for women (F:M 2:1). Of interest, this is a similar demographic to pseudotumour cerebri, which is believed to be an unrecognised predisposing factor. Epidemiology of secondary intracranial hypotension is variable and matches that of the underlying cause. Intracranial hypotension can broadly be divided into: 1.Primary: usually referred to as spontaneous intracranial hypotension. 2. Secondary: iatrogenic (LP or surgery), over shunting due to diversion devices or traumatic. Generally, there are no localising symptoms forms directly from the leak, as CSF is absorbed into tissues. The condition often presents as a positional headache which is relieved by a recumbent position, usually within 15-30min. It is confirmed by assessing opening pressure on LP (less than 7 cm CSF). Note that when this is done fluoroscopically, it should be performed in a lateral position to allow for accurate measurement of pressure. Occasionally presentation is more sinister, with even decreased level of consciousness and coma reported. Suggest update to description DOID:4723 Craniospinal Hypotension Decreased Intracranial Pressure Intracranial Hypotension SCDO:0000657 The hydrostatic pressure of venous blood in the marrow of bones. Term should be requested for inclusion into the "Ontology of Biological Attributes", perhaps in an appropriate location under "organ system trait". Or perhaps below "bone measurement" or "bone marrow measurement" in the CMO? http://medical-dictionary.thefreedictionary.com/intraosseous http://www.ncbi.nlm.nih.gov/pubmed/6456552 None IOP Intraosseous Pressure SCDO:0000665 A hypoperfusion of the blood through an organ or tissue caused by a pathologic constriction or obstruction of its blood vessels, or an absence of blood circulation. Should this be under "Abnormal Cardiovascular System Morphology" or ""Abnormal Cardiovascular System Physiology"? http://purl.bioontology.org/ontology/MESH/D007511 Sufficient SCDO:0000665 MESH:D007511 Ischemias Ischemia SCDO:0000666 Electrophoresis in which a pH gradient is established in a gel medium and proteins migrate until they reach the site (or focus) at which the pH is equal to their isoelectric point. Perhaps change label to "Hemoglobin Isoeletcric Focusing"? Exactsynonym "Hb IEF". See dc:source provided. http://purl.bioontology.org/ontology/MESH/D007525 Sufficient SCDO:0000666 MESH:D007525 Electrofocusing IEF Isoelectric Focusing SCDO:0000676 Laboratory tests used to evaluate how well the kidneys are working through examination of blood and urine. http://purl.bioontology.org/ontology/MESH/D007677 Sufficient SCDO:0000676 MESH:D007677 Kidney Function Tests Renal Function Test Renal Function Tests Kidney Function Test SCDO:0000677 A specialized area of medicine in which exercise and movement are used as the primary form of rehabilitation. Request inclusion into relevant ontology http://medical-dictionary.thefreedictionary.com/kinesiotherapy Few but definitions not freely available SCDO (Jade Hotchkiss) Kinesiotherapy SCDO:0000678 Collections of facts, assumptions, beliefs and practices that health professionals hold about the aetiology, pathophysiology, quality management of SCD and related social support systems based on global standards. Probably too specific to SCD to be included in other ontologies. https://www.ncbi.nlm.nih.gov/mesh/?term=base%2C+knowledge; https://www.ncbi.nlm.nih.gov/pubmed/20353928 None SCDO Knowledge about Sickle Cell Disease SCDO:0000682 The level of lactate dehydrogenase, an enzyme released during tissue damage and injury, found in a specified biological specimen. Request inclusion into relevant ontology Should this term's name be changed to "L-Lactate Dehydrogenase Level"? Few but definitions not freely available SCDO (Jade Hotchkiss) LD Level LDH Level Lactate Dehydrogenase Levels Lactic Acid Dehydrogenase Level Normal and abnormal ranges given here: https://www.healthline.com/health/lactate-dehydrogenase-test#results Lactate Dehydrogenase Level SCDO:0000683 A bioassay to measure levels of lactate dehydrogenase, an enzyme released during tissue damage and injury. Suggest update to label in PhenX (from "Lactate Dehydrogenase Level"). Suggest update to label phenX:811001 LDH Test Lactate Dehydrogenase Level Test Lactic Acid Dehydrogenase Test Lactate Dehydrogenase Test SCDO:0000685 Ulceration of the skin and underlying structures of the lower extremity. About 90% of the cases are due to venous insufficiency (varicose ulcer), 5% to arterial disease, and the remaining 5% to other causes. http://purl.bioontology.org/ontology/MESH/D007871 Sufficient SCDO:0000685 MESH:D007871 Leg Ulcers Leg Ulcer SCDO:0000689 Typical way of life or manner of living characteristic of an individual or group. (From APA, Thesaurus of Psychological Index Terms, 8th ed). http://purl.bioontology.org/ontology/MESH/D008019 Sufficient SCDO:0000689 MESH:D008019 Life Style Lifestyle SCDO:0000691 The coagulation of tissue by an intense beam of light, including laser (laser coagulation). In the eye it is used in the treatment of retinal detachments, retinal holes, aneurysms, hemorrhages, and malignant and benign neoplasms. (Dictionary of Visual Science, 3d ed) http://purl.bioontology.org/ontology/MESH/D008028 Sufficient SCDO:0000691 MESH:D008028 Light Coagulations Photocoagulation Photocoagulations Light Coagulation SCDO:0000694 Any process carried out to determine the condition of a patient's liver. http://bioportal.bioontology.org/ontologies/IDODEN?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FIDODEN_0003652 Sufficient SCDO:0000694 IDODEN:0003652 Liver Examination SCDO:0000698 Personality construct referring to an individual's perception of the locus of events as determined internally by his or her own behaviour versus fate, luck, or external forces. http://purl.bioontology.org/ontology/MESH/D007389 Sufficient SCDO:0000698 MESH:D007389 Control Locus External-Internal Control Health Locus of Control Internal-External Control Sense of Control Locus of Control SCDO:0000699 Studies in which variables relating to an individual or group of individuals are assessed over a period of time. http://purl.bioontology.org/ontology/MESH/D008137 Sufficient SCDO:0000699 MESH:D008137 Heart Study, Jackson Longitudinal Studies SCDO:0000702 A sampling methodology using small sample sizes when conducting surveys in small geographical or population-based areas or lots. http://purl.bioontology.org/ontology/MESH/D055810 Sufficient SCDO:0000702 MESH:D055810 LQAS Lot Quality Assurance Sampling SCDO:0000704 Measurement of the amount of air that the lungs may contain at various points in the respiratory cycle. Perhaps use the "DEFINITIONS AND SUBDIVISIONS OF LUNG VOLUME" section in the "Lung Function - Lung Volume #810401" protocol source in PhenX to include types of lung volume as subclasses. Can also use subclasses of Experimental Factor Ontology -- (EFO) term "pulmonary function measurement or sub-classes of "Lung Volume Measurements" in MESH. http://purl.bioontology.org/ontology/MESH/D008176 Sufficient SCDO:0000704 MESH:D008176 Lung Capacities Lung Capacity Lung Volume Lung Volume Measurements Lung Volume Measurement SCDO:0000705 Clinical assessment to determine the volume of gas within an individual's lung. Suggest update to label in PhenX (from "Lung Function - Lung Volume") Perhaps use the protocol source in PhenX to include different ways of measuring FRC (functional residual capacity) as subclasses (e.g. Measurement of FRC using body plethysmography, Measurement of FRC using nitrogen washout, Measurement of FRC using helium dilution, Measurement of lung volume using imaging techniques). SNOMED has more terms below "Lung Volume Test" Link to necessary medical device. PhenX protocol: Protocol - Lung Function - Lung Volume #810401 Suggest update to label phenX:810401 Lung Function - Lung Volume Lung Volume Assay Pulmonary Volume Assay Pulmonary Volume Test Lung Volume Test SCDO:0000706 'The lymphatic system in vertebrates is a network of conduits that carry a clear fluid called lymph. It also includes the lymphoid tissue through which the lymph travels. Lymphoid tissue is found in many organs, particularly the lymph nodes, and in the lymphoid follicles associated with the digestive system such as the tonsils. The system also includes all the structures dedicated to the circulation and production of lymphocytes, which includes the spleen, thymus, bone marrow and the lymphoid tissue associated with the digestive system. [Curator team: []]' http://purl.obolibrary.org/obo/UBERON_0002465 UBERON:0002465 obsolete Lymphoid System true SCDO:0000709 The use of drugs or other agents to prevent malarial infection. Examples: Proguanil, mefloquine, artesunate, insect repellant, insecticide-treated-bednet. Request inclusion into relevant ontology http://www.cdc.gov/malaria/travelers/drugs.html Few but definitions not freely available Malaria Prevention Malaria Prophylaxis SCDO:0000710 An instrument that is used for measuring the pressure of liquids and gases. Request inclusion into "Eagle-I Research Resource Ontology", below the "instrument" term. Perhaps the specific manometer used for measuring "Intraosseous Pressure" should be added as a sub-class and linked to directly. The American Heritage Science Dictionary. Retrieved October 20, 2016 from Dictionary.com website http://www.dictionary.com/browse/manometer Negligable Manometer SCDO:0000711 The current marital status of the respondent's caregiver (i.e. family member or another individual who takes primary responsibility for the respondent). Request inclusion into MESH below "Family Characteristics". PhenX protocol: Marital Status of Primary Caregiver #840101 Negligable phenX:840101 Marital Status of Primary Caregiver SCDO:0000725 A questionnaire to capture the frequency of acute pain episodes within a defined time frame due to sickle cell disease (SCD). It includes three self-administered questions from the Cooperative Study of Sickle Cell Disease (CSSCD) that capture number of painful episodes that required visits to the emergency room or hospital or interfered with daily activities. Suggest update to label in PhenX as we have done here because we have used "Frequency of Sickle Cell Pain Episodes Per Year" for the Diagnostic Instrument Measurement. PhenX protocol: Frequency of Sickle Cell Pain Episodes Per Year #830101 Suggest update to label phenX:830100 Measure of Frequency of Sickle Cell Pain Episodes SCDO:0000726 Measure of disease specific stigma based on patient reported outcome measurements that assesses 4 MoSCS factors: Social exclusion, Internalized Stigma, Expected Discrimination and Disclosure concerns. Measure includes stigma scores; perceived disease severity, acute care service utilization, hospital admission levels. N=262. Request inclusion into NCIT below "Research or Clinical Assessment Tool". J Health Psychol. 2016 May; 21(5): 808–820. African-Americans Patient Reported Outcome Adults with Sickle Cell Disease Adults 18 years and older None Bediako, Shawn M et al. “The Measure of Sickle Cell Stigma: Initial Findings from the Improving Patient Outcomes through Respect and Trust Study.” Journal of health psychology (2014): 1359105314539530. PMC. Web. 13 Mar. 2016. PMCID: PMC4627860 Measure of Sickle Cell Stigma MoSCS Measure of Sickle Cell Stigma (MoSCS) SCDO:0000727 The weight of the participant in kilograms. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) Measured Weight SCDO:0000728 An information entity used in the diagnosis of medical conditions. It could be the recording of the output of a diagnostic device or the outcome of a diagnostic tool. Request inclusion into relevant ontology. None SCDO (Jade Hotchkiss) Diagnostic Quantitative Measurement Diagnostic Measurement SCDO:0000737 The MOS Social Support Survey is a self-administered questionnaire that includes 19 items across four functional support subscales: emotional/informational support (8 items), tangible/instrumental support (4 items), affectionate support (3 items), and positive social interaction (3 items). Each item is scored on a 5-point Likert style scale (1 = None of the Time; 5 = All of the Time) to indicate how often that type of support is available to them. A score for each social support subscale can be computed by averaging across the individual items or by adding scores individual items together. Higher scores indicate more support. Check and show which source was used for the description and whether the description was adapted from the source. Suggest update to description in NCIT for "Medical Outcomes Study Social Support Survey". Sherbourne CD, Stewart A. The MOS Social Support Survey. Social Science and Medicine, v. 32, 1991, pp. 705-714. Sherbourne, Cathy D. and Anita Stewart. The MOS Social Support Survey. Santa Monica, CA: RAND Corporation, 1993. Multiple countries and cultural groups Self Clinic patients Adults 18 years and older no Suggest update to description NCIT:C110969 MOS Social Support Survey Medical Outcomes Study Social Support Survey Medical Outcomes Study (MOS) Social Support Survey SCDO:0000738 Recording of pertinent information concerning patient's illness or illnesses. http://purl.bioontology.org/ontology/MESH/D008499 Sufficient SCDO:0000738 MESH:D008499 Medical Records SCDO:0000739 Voluntary cooperation of the patient in taking drugs or medicine as prescribed. This includes timing, dosage, and frequency. http://purl.bioontology.org/ontology/MESH/D055118 Sufficient SCDO:0000739 MESH:D055118 Medication Adherence SCDO:0000740 A record of the type and dosage of all prescription and over-the-counter medications as well as dietary supplements currently being taken by the individual. Request inclusion into relevant ontology Would it also be appropriate to add this to "Diagnostic Instrument" below "Diagnostics"? PhenX protocol: Medication Inventory #140301 Negligable SCDO (Jade Hotchkiss) Medication Inventory SCDO:0000741 A state of consciousness in which the individual eliminates environmental stimuli from awareness so that the mind can focus on a single thing, producing a state of relaxation and relief from stress. A wide variety of techniques are used to clear the mind of stressful outside interferences. It includes meditation therapy. (Mosby's Medical, Nursing, and Allied Health Dictionary, 4th ed) http://purl.bioontology.org/ontology/MESH/D019122 Sufficient SCDO:0000741 MESH:D019122 Transcendental Meditation Meditation SCDO:0000742 A phospholipid-interacting antimalarial drug (antimalarials). It is very effective against plasmodium falciparum with very few side effects. Sufficient SCDO:0000742 MESH:D015767 Lariam Mephloquine WR142,490 Mefloquine SCDO:0000743 A type of glomerulonephropathy characterized by histology with thickening of the basement membrane and deposition of immune complexes in the subepithelial space. Suggest update to description in HPO Typically seen in adult population; rare in children. Idiopathic - may be related to M-type phosplipase A2 receptor antibodies; secondary forms may be related to autoimmune disease, underlying maligancies, drugs or infections. Has been reported in patients with sickle cell disease. Nephrotic syndrome with histologic features specific to membranous nephropathy. Suggest update to description HP:0012578 MN Membranous Glomerulopathy Membranous Nephropathy SCDO:0000746 Emotional, psychological, and social well-being of an individual or group. Sufficient SCDO:0000746 MESH:D008603 Emotional Health Mental Hygiene Mental Health SCDO:0000747 Works consisting of studies using a quantitative method of combining the results of independent studies (usually drawn from the published literature) and synthesizing summaries and conclusions which may be used to evaluate therapeutic effectiveness, plan new studies, etc. It is often an overview of clinical trials. It is usually called a meta-analysis by the author or sponsoring body and should be differentiated from reviews of literature. http://purl.bioontology.org/ontology/MESH/D017418 Sufficient SCDO:0000747 MESH:D017418 Meta-Analysis SCDO:0000748 The state of the chemical reactions that occur within the cells, tissues, or an organism. These processes include both the biosynthesis (anabolism) and the breakdown (catabolism) of organic materials utilized by the living organism. Request inclusion into relevant ontology. Add as sub-classes: Metabolic Function Normal and Metabolic Function Abnormal? (from SNOMED CT) http://purl.bioontology.org/ontology/MESH/D008660 None MESH:D008660 Metabolic Function Metabolic State SCDO:0000753 The presence of methemoglobin in the blood, resulting in cyanosis. A small amount of methemoglobin is present in the blood normally, but injury or toxic agents convert a larger proportion of hemoglobin into methemoglobin, which does not function reversibly as an oxygen carrier. Methemoglobinemia may be due to a defect in the enzyme NADH methemoglobin reductase (an autosomal recessive trait) or to an abnormality in hemoglobin M (an autosomal dominant trait). (Dorland, 27th ed) http://purl.bioontology.org/ontology/MESH/D008708 Sufficient SCDO:0000753 MESH:D008708 MetHb Methemoglobinemia SCDO:0000754 'Any procedure or test to diagnose a disease or disorder. [Curator team: []]' Perhaps move other sibling classes below this class? (Imaging Test/Diagnostic Imaging, -- -- Include sub-class "Biopsy" and include specific types below that? http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C18020 NCIT:C18020 Diagnostic Procedure deprecated Diagnostic Method true SCDO:0000760 A questionnaire to assess migraines and headaches. Suggest update to label in PhenX (from "Migraine") as we have done. Suggest update to label phenX:130500 Headache Disability Questionnaire Migraine Questionnaire SCDO:0000762 Transportable radiographic equipment allowing imaging services to be brought to the patient. Request inclusion into relevant ontology http://www.who.int/medical_devices/innovation/hospt_equip_26.pdf https://radiologykey.com/mobile-radiography/ None SCDO Mobile Radiographic Unit SCDO:0000763 Difficulty moving from place to place or from one position to another without assistance. Suggest update to description in MESH. http://purl.bioontology.org/ontology/MESH/D051346 Suggest update to description MESH:D051346 Ambulation Difficulty Ambulatory Difficulty Difficulty Ambulation Difficulty Walking Mobility Limitations Mobility Limitation SCDO:0000765 The biological processes, properties, and objects that are involved in maintaining, expressing, and transmitting from one organism to another, genetically encoded traits. Sufficient SCDO:0000765 MESH:D055614 Concepts, Genetic Genetic Phenomena SCDO:0000766 http://bioportal.bioontology.org/ontologies/ADO/?p=classes&conceptid=http%3A%2F%2Fscai.fraunhofer.de%2FAlzheimerOntology%23Modifying_the_home_enviornment_and_make_it_safer_for_the_patient obsolete Modifying the Home Environment and Making it Safer For the Patient true SCDO:0000771 The principal alkaloid in opium and the prototype opiate analgesic and narcotic. Morphine has widespread effects in the central nervous system and on smooth muscle. Sufficient SCDO:0000771 MESH:D009020 17-methyl-7,8-didehydro-4,5alpha-epoxymorphinan-17-ium-3,6alpha-diol Morphia Morphium Morphine SCDO:0000774 'A work that reports on a study executed by several cooperating institutions. [Curator team: []]' http://purl.bioontology.org/ontology/MESH/D016448 MESH:D016448 obsolete Multicenter Study true SCDO:0000775 Works about controlled studies which are planned and carried out by several cooperating institutions to assess certain variables and outcomes in specific patient populations, for example, a multicenter study of congenital anomalies in children. Sufficient SCDO:0000775 MESH:D015337 Multicenter Trial Multicenter Trials Multicentre Studies as Topic Multicentre Trial Multicentre Trials Multicenter Studies as Topic SCDO:0000776 The multidimensional health locus of control (MHLC) scale is a widely used measure of the factors that people believe exert some measures of control over their health. The MHLC originally developed by Wallston and colleagues contained 3 subscales describing various types of control-related cognitions an individual may have about the current state of his or her health. These were: Internal Health Locus of Control (IHLC), Powerful Others Health Locus of Control (PHLC) and Chance Health Locus of Control (CHLC). Subsequently, a fourth subscale, the God Locus of Health Control (G LHC) scale was developed to assess the extent of an individual's belief that God controls his or her health status was added to the measure. Thus, the expanded MHLC Consists of 4 sub-scales: one Internal and 3 external subscales namely, powerful others, chance and God. Each of the 4 sub-scales has 6 items making a total of 24 items. The two original versions of the MHLC (forms A & B) deal with the general health status whereas the third version (Form C) assesses control-related cognitions about a specific disease state. Request inclusion into NCIT below "Research or Clinical Assessment Tool". Multiple countries and cultural groups Self Healthy population and patients with specific medical conditions Spanish; Chinese; Persian Has adequate construct validity and acceptable metric properties 15 years and above no Few but definitions not freely available Wallston K., Wallston B. and De Vellis R. (1978). Development of the multidimensional health locus of control (MHLC) scales. Health Education Monographs, 6, 160-169. Wallston KA, Malcarne VL, Flores L, Hansdottir I, Smith CA, Stein MJ, Weisman MH, Clements PJ. Does God Determine Your Health? The God Locus of Health Control Scale. Cognitive Therapy and Research . April 1999, Volume 23 (2):131-142. MHLC MHLC Scales Multidimensional Health Locus of Control Scales Multidimensional Health Locus of Control Scales (MHLC) SCDO:0000777 The presence of skeletal muscular atrophy, reduction in the muscle bulk. Suggest update to description in HPO. Provide source for additional info. http://purl.obolibrary.org/obo/HP_0003202 Suggest update to description HP:0003202 Amyotrophy Muscle Wasting Muscular Atrophy Neurogenic Muscle Atrophy Skeletal Muscle Atrophy Muscle Atrophy SCDO:0000780 Anatomical system that consists of the muscular and skeletal systems. http://purl.obolibrary.org/obo/UBERON_0002204 UBERON:0002204 Musculo-Skeletal System deprecated Musculoskeletal System true SCDO:0000781 The process of identifying carriers/heterozygotes of a genetic mutation that can result in a severe recessive condition. Carrier screening is done using various laboratory techniques. Request inclusion into relevant ontology (MESH) or suggest inclusion of description in NCIT. Alswaidi, F.M. and O'brien, S.J., 2009. Premarital screening programmes for haemoglobinopathies, HIV and hepatitis viruses: review and factors affecting their success. Journal of medical screening, 16(1), pp.22-28. Few but definitions not freely available SCDO (Clair Ingram) MESH:D006580 Mutation Carrier Detection This term is very similar to but different (more specific) from the term "Genetic Carrier Screening" in MESH. Mutation Carrier Screening SCDO:0000782 This gene encodes a protein with three HTH DNA-binding domains that functions as a transcription regulator. This protein plays an essential role in the regulation of hematopoiesis. This gene may be aberrently expressed or rearranged or undergo translocation in leukemias and lymphomas, and is considered to be an oncogene. Alternative splicing results in multiple transcript variants. Exists in other ontologies but we have provided a description more relevant to its relationship with SCD. Link to "Hereditary Persistence of fetal hemoglobin". http://www.ncbi.nlm.nih.gov/gene/4602 Not relevant to context of sickle cell MYB Gene MYB Proto-Oncogene, Transcription Factor MYB-HSP1 MYB SCDO:0000787 A bioassay to determine an individual's level of N-terminal pro-brain natriuretic peptide (NT-proBNP). Label different from source's "N-terminal Pro-brain Natriuretic Peptide (NT-proBNP)" Suggest update to label phenX:810501 NT-proBNP Test Equipment needed: Phlebotomy supplies, centrifuge for serum separation, and freezer for sample storage is required. N-terminal Pro-brain Natriuretic Peptide Test SCDO:0000789 A specific opiate antagonist that has no agonist activity. It is a competitive antagonist at mu, delta, and kappa opioid receptors. Are the synonyms included relevant to SCD? Should other synonyms from the description source be included? Sufficient SCDO:0000789 MESH:D009270 1-N-Allyl-14-hydroxynordihydromorphinone 17-allyl-3,14-dihydroxy-4,5α-epoxymorphinan-6-one MRZ-2593 Naloxone SCDO:0000791 Drugs designed to treat inflammation of the nasal passages, generally the result of an infection (more often than not the common cold) or an allergy related condition, e.g., hay fever. The inflammation involves swelling of the mucous membrane that lines the nasal passages and results in inordinate mucus production. The primary class of nasal decongestants are vasoconstrictor agents. (From PharmAssist, The Family Guide to Health and Medicine, 1993) Sufficient SCDO:0000791 MESH:D014663 Nasal Vasoconstrictor Agents Nasal Vasoconstrictors Nasal Decongestants SCDO:0000794 'A subspecialty of internal medicine concerned with the anatomy, physiology, and pathology of the kidney. [Curator team: []]' http://purl.bioontology.org/ontology/MESH/D009398 MESH:D009398 obsolete Nephrology true SCDO:0000796 Nephrotic syndrome is a collection of findings resulting from glomerular dysfunction with an increase in glomerular capillary wall permeability associated with pronounced proteinuria >3.5 g per 24 hours (in children, >40 mg/m2/hr or PCR >2000 mg/g [>200 mg/mmol] or >300 mg/dl or 3+ on urine dipstick) plus hypoalbuminemia (<3gm/dl) and edema. Suggest update to description in the HPO Nephrotic syndrome related to sickle cell disease typically occurs in adulthood and preceded by lesser degree of proteinuria, other forms may occur at any age with different histologic lesions occurring at different ages. Variety of causes - in sickle cell disease, most common lesion is focal segmental glomerulosclerosis (FSGS). Other causes may be other forms of primary glomerular disease including membranous nephropathy, minimmal change disease, membranoproliferative glomerulonephritis. Secondary forms may result from diabetes, amyloidosis. Heavy proteinuria, edema, hyperlipidemia. May also be associated with hypertension and increased risk of venous thrombosis. Suggest update to description HP:0000100 Nephrosis Nephrotic Syndrome SCDO:0000797 Severely increased amount of excretion of protein in the urine, defined as 3.5 grams per day or more in adults and 40 mg per meter-squared body surface area per hour in children, or urine protein to creatinine ratio >2000 mg/g [>200 mg/mmol] in children. Suggest update to description in HPO. In sickle cell disease, seen primarily in adult population but may develop in childhood if secondary cause occurs. Glomerular diseases that lead to protein loss in the urine (See Nephrotic Syndrome). Severely increased amount of excretion of protein in the urine, defined as 3.5 grams per day or more in adults and 40 mg per meter-squared body surface area per hour in children, or urine protein to creatinine ratio >2000 mg/g [>200 mg/mmol] in children. Suggest update to description HP:0012593 Nephrotic-Range Proteinuria Is diagnosed by assessment of proteinuria (see Proteinuria) by 24hr urine collection or by urine protein-creatinine ratio on spot urine sample [KDIGO 2012]. Nephrotic Range Proteinuria SCDO:0000798 The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior. http://purl.obolibrary.org/obo/UBERON_0001016 UBERON:0001016 Neurological System deprecated Nervous System true SCDO:0000799 An invisible complication of sickle cell anemia (SSA) that defies detection by imaging and other routine diagnostic methods. Impaired neurocognitive function in seemingly neurologically intact patients is not related to vasoocclusion or hemolysis. It is detected by neuropsychiatric and neurobehavioral testing and is associated with anemia and age. Request inclusion into relevant ontology http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3415156/ None SCDO Neurocognitive Impairment SCDO:0000801 Physician-supervised programs designed to rehabilitate people with diseases, trauma, or disorders of the nervous system. http://purl.bioontology.org/ontology/MESH/D000066530 Sufficient SCDO:0000801 MESH:D000066530 Neurologic Rehabilitation Neurorehabilitation Rehabilitation, Neurologic Rehabilitation, Neurological Neurological Rehabilitation SCDO:0000803 Testing of neonates to identify those with major sickling diseases. Link to "Hb isoelectric focusing" and "HPLC fractionation" ? Request inclusion into relevant ontology. Perhaps in SNOMED CT below "Screening for sickle cell disease"? Newborn Screening for Sickle Cell Disease and Other Hemoglobinopathies. JAMA. 1987;258(9):1205–1209. doi:10.1001/jama.1987.03400090089040 None Newborn Infant Screening for Sickle Cell Neonatal Screening for Sickle Cell SCDO:0000804 A physical assessment of the various symptoms associated with a stroke, consisting of 11 categories. For each category, the test administrator asks the respondent to perform an activity or respond to stimuli. Respondents receive a score for each category based upon their ability to complete the activity or respond to the action. Each score typically ranges from 0 to 3. Each category of the NIHSS is designed to determine the respondent's level of consciousness (LOC), visual, motor, or language ability. http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820801 PhenX protocol: NIH Stroke Scale (NIHSS) #820801 18 years and older Examiners must be trained to administer, score, and interpret the NIH Stroke Scale (NIHSS). The National Institute of Neurological Disorders and Stroke (NINDS) provides a comprehensive interactive training DVD for the NIHSS. Information and purchasing details for this training are available on the NINDS website. Few but definitions not freely available phenX:820801 NIH Stroke Scale NIHSS NIH Stroke Scale (NIHSS) SCDO:0000807 Patients who do not turn up for scheduled healthcare appointments. http://purl.bioontology.org/ontology/MESH/D000067455 Sufficient SCDO:0000807 MESH:D000067455 No Show Patient Patient No Show Patient No-Show No-Show Patient SCDO:0000808 Frequent urination at night that interrupts sleep. It is often associated with outflow obstruction, diabetes mellitus, or bladder inflammation (cystitis). http://purl.bioontology.org/ontology/MESH/D053158 Sufficient SCDO:0000808 MESH:D053158 Nycturia Often occuring as a result of heart insufficiency. Nocturia SCDO:0000809 A subclass of analgesic agents that typically do not bind to opioid receptors and are not addictive. Many non-narcotic analgesics are offered as nonprescription drugs. http://purl.bioontology.org/ontology/MESH/D018712 Sufficient SCDO:0000809 MESH:D018712 Non-Narcotic Nonnarcotic Nonnarcotic Analgesic Nonnarcotic Opioid Nonopioid Non Opioid SCDO:0000810 A gene that does not encode a globin family protein. Perhaps too specific to the SCDO to be included in other ontologies? None SCDO (Jade Hotchkiss) Non-Globin Gene SCDO:0000811 Sickle retinopathy caused by direct damage or remodeling of the small blood vessels supplying the retina secondary to vaso-occlusion and local ischemia. Request inclusion into HPO below "Retinopathy/Sickle Retinopathy". http://en.wikipedia.org/wiki/Retinopathy http://eyewiki.aao.org/Sickle_Cell_Retinopathy None SCDO (Jade Hotchkiss) Non-Proliferative Sickle Retinopathy SCDO:0000812 Includes acute respiratory episodes with lower respiratory tract signs that do not meet the criteria for other diagnoses. May include episodes which would have been diagnosed as ACS were radiographic facilities available. Request inclusion into relevant ontology Provide source for additional info. Several possible etiologies including infections by various classes of microorganisms, pulmonary fat emobolism, infarction and pulmonary embolism. Acute onset of respiratory symptoms and signs including cough, coryza +/- fever. None SCDO Non-specific Acute Lower Respiratory Tract Episode SCDO:0000818 'A work that reports on the results of a clinical study in which participants may receive diagnostic, therapeutic, or other types of interventions, but the investigator does not assign participants to specific interventions (as in an interventional study). [Curator team: []]' http://purl.bioontology.org/ontology/MESH/D064888 MESH:D064888 obsolete Observational Study true SCDO:0000819 Works about clinical studies in which participants may receive diagnostic, therapeutic, or other types of interventions, but the investigator does not assign participants to specific interventions (as in an interventional study). http://purl.bioontology.org/ontology/MESH/D064887 Sufficient SCDO:0000819 MESH:D064887 Observational Studies as Topic SCDO:0000822 Skilled treatment that helps individuals achieve independence in all facets of their lives. It assists in the development of skills needed for independent living. http://purl.bioontology.org/ontology/MESH/D009788 Sufficient SCDO:0000822 MESH:D009788 Occupational Therapies Therapies, Occupational Therapy, Occupational Occupational Therapy SCDO:0000828 Low output of urine, defined as an output below 5mL/kg/hr over 6 hours. Suggest update to description in HPO Suggest update to description HP:0100520 Reduced Urine Output Oliguria SCDO:0000833 Surgery performed on the eye or any of its parts. http://purl.bioontology.org/ontology/MESH/D013508 Sufficient SCDO:0000833 MESH:D013508 Ophthalmologic Surgical Procedures Ophthalmological Surgical Procedure Ophthalmologic Surgical Procedure SCDO:0000834 Device for examining the interior of the eye, permitting the clear visualization of the structures of the eye at any depth. http://purl.bioontology.org/ontology/MESH/D019721 Sufficient SCDO:0000834 MESH:D019721 Funduscope Ophthalmoscopes Ophthalmoscope SCDO:0000835 Examination of the interior of the eye with an ophthalmoscope. Include "Direct Ophthalmoscopy" and "Indirect Ophthalmoscopy" from NCIT as sub-classes? (Direct could be used to diagnose "Conjunctival Comma Sign") http://purl.bioontology.org/ontology/MESH/D009887 Sufficient SCDO:0000835 MESH:D009887 Ophthalmoscopy SCDO:0000839 A general term for bone weakness owing to a defect in mineralization of the protein framework known as osteoid. This defective mineralization is mainly caused by lack in vitamin D. Osteomalacia in children is known as rickets. Suggest update to description in HPO. (remove "Osteomalacia" from start of definitiion) Provide source for additional info. http://purl.obolibrary.org/obo/HP_0002749 Abnormal vitamin D metabolism: 1) Deficient intake or absorption;2) Defective 25-hydroxylation due to biliary cirrhosis- alcoholic cirrhosis- anticonvulsants; 3) Loss of vitamin D binding protein- nephrotic syndrome; 4) Defective 1-alpha 25-hydroxylation: Hypoparathyroidism, Renal failure, Vitamin D-dependent rickets type 1; 5) Defective target organ response to calcitriol: Vitamin D-dependent rickets, type II (Hereditary vitamin D resistant rickets, HVDRR). Mineralization defects: 1) Abnormal matrix: Chronic renal failure, Osteogenesis imperfecta, Fibrogenesis imperfecta, Axial osteomalacia; 2) Enzyme deficiency: Hypophosphatasia; 3) Mineralization inhibitors: bisphosphonates, Aluminum, fluoride. Phosphate deficiency: 1) Decreased intake ( antiacids); 2) Impaired renal reabsorption, that can be Primary defects = X-linked hypophosphatemic rickets (vitamin D resistant rickets, VDRR), Hereditary hypophosphatemic rickets with hypercalciuria, Sporadic acquired hypophosphatemic rickets, Fanconi syndrome, Wilson disease, cystinosis, multiple myeloma; or can be Secondary defects = 2) Secondary hyperparathyroidism (renal tubular acidosis, type 1 and disorders of vitamin D metabolism), 2) Oncogenic osteomalacia. May be asymptomatic and present radiologically as osteopenia. Or it may present as diffuse bone and joint pain, muscle weakness, and difficulty walking, Fractures, Muscle spasms, cramps. Suggest update to description HP:0002749 Adult Rickets Osteomalacia SCDO:0000840 An inflammatory process accompanied by bone destruction and caused by an infecting microorganism. Suggest update to description in HPO (remove "Osteomyelitis is" from the start of the definition. Provide source for additional info. http://purl.obolibrary.org/obo/HP_0002754 Bacteria, blunt trauma, fracture, bone surgery. Tenderness, redness, and warmth in the area of infection, fever, fatigue, bone pain, swelling around the affected bone, lost range of motion. Suggest update to description HP:0002754 Bone Infection Osteomyelitis can be acute or chronic and can be caused by a variety of microbial agents. Osteomyelitis SCDO:0000849 The amount of oxygen bound to hemoglobin in arterial blood expressed as a percentage of the maximal binding capacity, as determined by an arterial blood gas test. Request inclusion into CMO below "Oxygen Saturation" Few but definitions not freely available Arterial HbO2 Arterial Oxyhemoglobin Saturation Arterial SaO2 Arterial Sats HBOXHGB Oxygen Saturation of Arterial Blood Oxyhemoglobin to Total Hemoglobin Ratio Measurement Oxyhemoglobin/Total Hemoglobin Arterial Oxygen Saturation SCDO:0000851 An unpleasant sensory and emotional experience triggered in the nervous system, associated with actual or potential tissue damage, or described in terms of such damage. Suggest update to description in HPO. Provide source for additional info. http://purl.obolibrary.org/obo/HP_0012531 Somatic pain is caused by injury to skin, muscles, bone, joint, and connective tissues. Deep somatic pain is usually described as dull or aching, and localized in one area. Visceral pain refers to pain that originates from ongoing injury to the internal organs or the tissues that support them. Somatic pain from injury to the skin or the tissues just below it often is sharper and may have a burning or pricking quality. Nociceptive pain is believed to be caused by the ongoing activation of pain receptors in either the surface or deep tissues of the body. There are two types: "somatic" pain and "visceral" pain. Neuropathic pain is believed to be caused by changes in the nervous system that sustain pain even after an injury heals. "Psychogenic" pain is a simple label for all kinds of pain that can be best explained by psychological problems. Suggest update to description HP:0012531 Pain SCDO:0000852 The impact of sickle cell pain on the daily activities of patients. The degree to which pain interferes with their quality of life. This pain is related to the unique features of Sickle Cell Disease. Request inclusion into relevant ontology None SCDO Pain Burden Pain Disability Pain Impact Pain Interference Pain Status SCDO:0000864 A method of determining the shape and consistency of the liver by feeling with the fingers or hands. Request inclusion into relevant ontology Few but definitions not freely available SCDO (Jade Hotchkiss) Liver Palpation Palpation of Liver SCDO:0000866 Invertebrate organisms that live on or in another organism (the host), and benefit at the expense of the other. Traditionally excluded from definition of parasites are pathogenic bacteria; fungi; viruses; and plants; though they may live parasitically. http://purl.bioontology.org/ontology/MESH/D010271 Sufficient SCDO:0000866 MESH:D010271 Parasites Parasite SCDO:0000869 Voluntary cooperation of the patient in following a prescribed regimen. http://purl.bioontology.org/ontology/MESH/D010349 Sufficient SCDO:0000869 MESH:D010349 Adherence Patient Adherence Patient Cooperation Patient Compliance SCDO:0000873 A headache disability questionnaire which is completed by the patient and his/her parent and is reviewed with the clinician or study staff. It captures the impact of headaches on school performance (three questions), activities at home (one question on homework or chores), and social and/or sports functions (two questions). It is scored by summing the answers across the six questions. If a range is provided as an answer, either use the high end of the range or prompt for a single answer. The frequency and severity are not scored but can be used for clinical reference. Suggest update to label in PhenX (from "Migraine - Children") as we have done. PhenX protocol: Migraine - Children #130502 Suggest update to label phenX:130502 PedMIDAS Pediatric Migraine Questionnaire Pediatric Migraine Disability Assessment SCDO:0000874 A physical assessment of the various symptoms associated with a stroke, consisting of eleven categories. The PedNIHSS was developed by a panel of pediatric and adult stroke experts and is a modification of the adult NIH stroke scale (NIHSS). Modifications were made to allow individuals age 18 or younger to be assessed and are identified in the PedNIHSS by bold italic text. http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820802 PhenX protocol: Pediatric NIH Stroke Scale (PedNIHSS) #820802 2-18 years old Examiners must be trained to administer, score, and interpret the NIHSS. The National Institute of Neurological Disorders and Stroke (NINDS) provides a comprehensive interactive training DVD for the National Institutes of Health Stroke Scale (NIHSS). Information and purchasing details for this training is available on the NINDS website. None phenX:820802 PedNIHSS Pediatric NIH Stroke Scale For each category of the PedNIHSS, the examiner asks the respondent to perform an activity or respond to an action by the provider. Respondents receive a score for each category based upon their ability to complete the activity or respond to the action. Each score typically ranges from 0 to 3. Each category of the PedNIHSS is designed to determine the respondent’s level of consciousness (LOC), visual, motor, or language ability. Pediatric NIH Stroke Scale (PedNIHSS) SCDO:0000876 A questionnaire to assess educational performance and learning accommodations. Suggest update to label in PhenX as we have done. PhenX protocol: Pediatric School Performance #840201 Many rare genetic conditions (e.g., sickle cell disease) and other diseases are associated with developmental delays, damage to the central nervous system, and frequent absences from school due to illness, all of which can impact school performance. Suggest update to label phenX:840200 Pediatric School Performance Measure SCDO:0000877 A generic symptom-specific instrument to measure fatigue across pediatric populations. Request inclusion into NCIT below "Pediatric Quality of Life Inventory". Panepinto JA, Torres S, Bendo CB, McCavit TL, Dinu B, Sherman-Bien S, Bemrich-Stolz C, Varni JW (2014). PedsQL Multidimensional Fatigue Scale in sickle cell disease: feasibility, reliability, and validity. Pediatric Blood & Cancer, 61,171-177 Self; Proxy (Parent report) Clinic patients Validation study in SCD Children 2 - 18 (child report ages 5 - 18 years; parent proxy report of children ages 2 - 18 years) None The 18-item PedsQL Multidimensional Fatigue Scale encompasses three domains: 1) General Fatigue, 2) Sleep/Rest Fatigue and 3) Cognitive Fatigue. The format, instructions, Likert response scale, and scoring method are identical to the PedsQL 4.0 Generic Core Scales [16], with higher scores indicating better HRQOL (lower fatigue symptoms). The instructions ask how much of a problem each item has been during the past one month. PedsQL Multidimensional Fatigue Scale SCDO:0000878 The PedsQL Sickle Cell Disease Module includes 43 items from 9 subscales: Pain and Hurt (9 items); Pain Impact (10 items); Pain Management and Control (2 items); Worry (5 items); Worry II (2 items); Emotions (2 items); Treatment (7 items); Communication I (3 items); and Communication II (3 items). For all ages, each item asks how much of a problem there has been in the past month. There are self- or parent-reported forms for ages 8 to 18, and responses are scored on a 5-point Likert-style scale (0 = never a problem; 1 = almost never a problem; 2 = sometimes a problem; 3 = often a problem; 4 = almost always a problem). Forms for children ages 5 to 7 are interviewer-administered, and responses include a 3-point Likert-style scale (0 = not at all a problem; 2 = sometimes a problem; 4 = a lot of a problem). Items are reversed-scored and converted to a 100-point scale (0 = 100, 1 = 75, 2 = 50, 3 = 25, 4 = 0) with higher scores indicating better quality of life. Scores for individual subscales are the sum of items divided by the total number or items answered. The total score for the PedsQL Sickle Cell Disease Module is the sum of the items divided by the number of items answered. Request inclusion into NCIT below "Pediatric Quality of Life Inventory". PhenX protocol: PedsQL Sickle Cell Disease Module #820202 Self; Proxy (Parent report) Clinic Patients (Children with SCD) Ages 2 to 18 No. The PedsQ Sickle Cell Disease Module is a proprietary instrument and administration requires permission and a license from the MAPI Research Trust. None Panepinto JA, Torres S, Bendo CB, McCavit TL, Dinu B, Sherman-Bien S, Bemrich-Stolz C, Varni JW (2013).PedsQL sickle cell disease module: feasibility, reliability, and validity.Pediatric Blood & Cancer, 60,1338-1344. PedsQL Sickle Cell Disease Module SCDO:0000881 Use of penicillin for the prevention of infections with penicillin-susceptible organisms, e.g. Streptococcus pneumoniae. Request inclusion into relevant ontology Few but definitions not freely available SCDO Penicillin Prophylaxis SCDO:0000882 A method of determining the size of the liver by tapping on the surface of the abdomen. To be requested for inclusion into SNOMED CT, below "Diagnostic procedure on liver". None SCDO (Jade Hotchkiss) Percussion of Liver SCDO:0000885 An estimation of the oxygen saturation level usually measured with a pulse oximeter device. Request inclusion into CMO below "Oxygen Saturation" http://en.wikipedia.org/wiki/Oxygen_saturation_(medicine) Few but definitions not freely available SNOMEDCT:431314004 Oxygen Saturation of Peripheral Blood Peripheral SaO2 Peripheral Sats Peripheral HbO2 Peripheral Oxyhemoglobin Saturation SpO2 Peripheral Oxygen Saturation SCDO:0000895 A (combination of) quality(ies) of some or all sickle cell disease individuals, determined by the interaction of the genetic make-up of these individuals (with regard to sickle cell disease) and their environment. Probably too specific to warrant inclusion into anther ontology. Make sure complications as described in "Definitions of the Phenotypic Manifestations of Sickle Cell Disease" (Ballas, 2010) are included in Phenotype. http://bioportal.bioontology.org/ontologies/OGMS?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOGMS_0000023 None SCDO OGMS:0000023 Phenotype of Sickle Cell Disease SCDO:0000896 The physical method (technology) used to measure / readout the effect caused by a perturbagen in the assay environment. Sufficient SCDO:0000896 BAO:0000035 Physical Detection Method SCDO:0000897 The part of the human environment that consists of purely physical factors, including the natural environment (such as soil, climate, water supply) and the built environment. Request inclusion into relevant ontology Physical Environment. Merriam-Webster.com. Merriam-Webster, n.d. Web. 9 Nov. 2016. Few but definitions not freely available Physical Environment SCDO:0000898 Systematic and thorough inspection of the patient for physical signs of disease or abnormality. http://purl.bioontology.org/ontology/MESH/D010808 Sufficient SCDO:0000898 MESH:D010808 Physical Assessment Physical Examination SCDO:0000900 One's ability to carry out activities that require physical actions, ranging from self-care (activities of daily living) to more complex activities that require a combination of skills, often within a social context. Physical function is inclusive of the term disability and includes the full spectrum of physical functioning from severe impairment to exceptional physical abilities. Determine and specify the description source. -- -- Include a term to do with level of independence? Few but definitions not specific enough SCDO Mobility Motor Function Physical Function Physical Health Physical Functioning SCDO:0000902 An organismal assay designed to capture information pertaining to the organic processes and phenomena of an organism or any of its parts or of a particular bodily process. http://purl.obolibrary.org/obo/ERO_0001292 Sufficient SCDO:0000902 ERO:0001292 Physiological Assay SCDO:0000903 A therapeutic intervention that remediates impairments and promotes mobility, function, and quality of life through examination, diagnosis, and physical intervention. http://purl.obolibrary.org/obo/OAE_0002476 Sufficient SCDO:0000903 OAE:0002476 Physical Therapy Physiotherapy SCDO:0000905 Small-scale tests of methods and procedures to be used on a larger scale if the pilot study demonstrates that these methods and procedures can work. http://purl.bioontology.org/ontology/MESH/D010865 Sufficient SCDO:0000905 MESH:D010865 Pilot Study Pilot Projects SCDO:0000908 A nonincisional procedure that has become a well-accepted alternative to scleral buckling and vitrectomy for the repair of selected cases of rhegmatogenous retinal detachment. Request inclusion into relevant ontology http://emedicine.medscape.com/article/1844217-overview Few but definitions not freely available Pneumatic Retinopexy SCDO:0000913 The process in which a DNA polymerase is used to amplify a piece of DNA by in vitro enzymatic replication. As the process progresses, the DNA thus generated is itself used as a template for replication. This sets in motion a chain reaction in which the DNA template is exponentially amplified. Suggest update to description in OBI http://purl.obolibrary.org/obo/OBI_0000415 Suggest update to description OBI:0000415 PCR Polymerase Chain Reaction SCDO:0000917 'Works about randomized clinical trials that compare interventions in clinical settings and which look at a range of effectiveness outcomes and impacts. [Curator team: []]' http://purl.bioontology.org/ontology/MESH/D065007 MESH:D065007 Pragmatic Clinical Trial true SCDO:0000919 Prenatal detection of a fetus affected with Sickle Cell Disease using appropriate laboratory techniques. Detection of affected fetuses allows couples to make informed decisions regarding the pregnancy. Request inclusion into relevant ontology. Perhaps in SNOMED CT below "Screening for sickle cell disease". None SCDO (Clair Ingram) Prenatal Screening for Sickle Cell SCDO:0000922 Activities to prevent Sickle Cell Disease or its complications. Probably too specific to SCD to be included in other ontologies. Consider making the description more generic (e.g. "Activities to prevent a disease or its complications.") None SCDO Preventive Therapeutics Prophylactic Therapeutics Preventative Therapeutics SCDO:0000923 A prolonged painful erection that may last hours and is not associated with sexual activity. It is seen in patients with sickle cell anemia, advanced malignancy, spinal trauma, and certain drug treatments. http://purl.bioontology.org/ontology/MESH/D011317 Sufficient SCDO:0000923 MESH:D011317 Priapism SCDO:0000924 Care which provides integrated, accessible health care services by clinicians who are accountable for addressing a large majority of personal health care needs, developing a sustained partnership with patients, and practicing in the context of family and community. This term is not below Quality of Health Care in MESH, but below "Health Services Administration" ---> "Patient Care Management" ---> "Comprehensive Health Care http://purl.bioontology.org/ontology/MESH/D011320 Sufficient SCDO:0000924 MESH:D011320 Primary Care Primary Health Care Primary Healthcare SCDO:0000925 A biguanide compound which metabolizes in the body to form cycloguanil, an anti-malaria agent. Cycloguanil stops the malaria parasite, Plasmodium falciparum and Plasmodium vivax, from reproducing once it is in the red blood cells. It does this by inhibiting the enzyme, dihydrofolate reductase, which is involved in the reproduction of the parasite. Suggest update to description in MESH Suggest update to description MESH:D002727 1-(P-Chlorophenyl)-5-isopropylbiguanide Chlorguanid Chlorguanide Chloroguanide N-(4-Chlorophenyl)-n'-(isopropyl)-imidodicarbonimidic diamide Proguanil SCDO:0000926 Sickle retinopathy that involves the upregulation of vascular growth factors due to chronic changes of local hypoxia and ischemia. Request inclusion into HPO below "Retinopathy/Sickle Retinopathy". http://eyewiki.aao.org/Sickle_Cell_Retinopathy None SCDO (Jade Hotchkiss) Retinopathy due to SCD Characterized by Neovascularization Sickle Cell Proliferative Retinopathy Proliferative Sickle Retinopathy SCDO:0000927 This protocol includes 29 self-administered quality of life-type questions from the PROMIS Profile 29 for adults. The quality of life questions include physical function, anxiety, depression, fatigue, sleep disturbance, ability to participate in social roles and activities, and pain intensity over the past 7 days. Each question, except for the pain intensity question, is measured on a 5-point scale. Suggest update to label in PhenX as we have done. http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=221302 PhenX protocol: Quality of Life - Adult #221302 Suggest update to label PROMIS 25 Profie v2.0 PROMIS Adult Profile 29 SCDO:0000928 This protocol includes 25 quality of life-type questions relating to physical function mobility, anxiety, depressive symptoms, fatigue, peer relationships, pain interference, and pain intensity over the past 7 days. Suggest update to label in PhenX as we have done. http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=221301 PhenX protocol: Quality of Life - Pediatric #221301 Suggest update to label PROMIS 25 PROMIS 25 Profie PROMIS Pediatric Profile 25 SCDO:0000930 A planned process that has the objective to reduce the risk of acquiring one or more infections. Few but definitions not freely available http://purl.obolibrary.org/obo/OGMS_0000103 Disease Prevention Infection Prophylaxis SCDO:0000931 Observation of a population for a sufficient number of persons over a sufficient number of years to generate incidence or mortality rates subsequent to the selection of the study group. http://purl.bioontology.org/ontology/MESH/D011446 Sufficient SCDO:0000931 MESH:D011446 Prospective Study Prospective Studies SCDO:0000932 Increased amounts of any protein (including albumin) in the urine - typically more than 300mg in a 24hr period. Suggest update to description in HPO. http://purl.obolibrary.org/obo/HP_0000093 In sickle cell disease, overt proteinuria (distinguised from albuminuria) may be noted in childhood although less common (4.5% in ages 2-21 [Wigfall 2000] v. 26% in adults [Guasch 2006]). At most severe form - lead to nephrotic syndrome. Caused by a variety of kidney diseases, including sickle cell disease, diabetes, glomerular disease, arteriosclerosis. Elevated amounts of protein in the urine - typically greater than 300mg in 24 hrs. Suggest update to description HP:0000093 High Urine Protein Levels Screening Recommendations: Screen all individuals with SCD, beginning by age 10, for proteinuria. If the result is negative, repeat screening annually. If the result is positive, perform a first morning void urine albumin-creatinine ratio and if abnormal, consult with or refer to a renal specialist. Proteinuria SCDO:0000934 This is a 17-item scale, separated into 4 subscales with good psychometric properties. Negative Attitudes Scale comprises six items grouped together (Mean=36.5, SD=21.9, Potential range = 0 to 100). Higher scores on this scale indicate an endorsement of more negative views about SCD patients. Positive Attitudes Scale comprises four items grouped together (Mean=45.7, SD=24.3, Potential range = 0 to 100). Higher scores indicate an endorsement of more positive views about SCD patients. Concern Raising Behaviors Scale comprises four items grouped together (Mean = 53.7, SD = 22.0, Potential range = 0 to 100). Higher scores indicate greater endorsement of the belief that certain SCD patient behaviors raise clinician concern that the patient is inappropriately drug-seeking. Red-Flag Behaviors Scale comprises three items grouped together (Mean = 58.7, SD = 22.7, Potential range = 0 to 100). Higher scores on this scale indicate greater endorsement of the belief that certain SCD patient behaviors raise clinician concern about patient drug-seeking. Request inclusion into NCIT below "Research or Clinical Assessment Tool". Haywood, Jr., C., Lanzkron, S., Hughes, MD3, Brown, R., Massa, M., Ratanawongsa, N., and Beach, MC. (2010). A Video-Intervention to Improve Clinician Attitudes Toward Patients with Sickle Cell Disease: The Results of a Randomized Experiment. J Gen Intern Med 26(5):518–23. African Americans Self Heath care providers Demonstrated validity with SCD populations in the US Adults None Haywood, Jr., C., Lanzkron, S., Hughes, MD3, Brown, R., Massa, M., Ratanawongsa, N., and Beach, MC. (2010). A Video-Intervention to Improve Clinician Attitudes Toward Patients with Sickle Cell Disease: The Results of a Randomized Experiment. J Gen Intern Med 26(5):518–23. Provider Attitudes Toward Patients with Sickle Cell Disease SCDO:0000935 Pruritus, or itch, is defined as an unpleasant sensation that provokes the desire to scratch. Suggest update to description. The current description seems to be describing two different things in the same description. Suggest update to description HP:0000989 Itchy Skin Skin Itching Pruritus SCDO:0000937 Stress wherein emotional factors predominate. Sufficient SCDO:0000937 MESH:D013315 Emotional Stress Life Stress Psychological Suffering Psychological Stress SCDO:0000938 The absence of appropriate stimuli in the physical or social environment which are necessary for the emotional, social, and intellectual development of the individual. This term is placed below "Culture" in MESH. http://purl.bioontology.org/ontology/MESH/D011610 Sufficient SCDO:0000938 MESH:D011610 Psychosocial Deprivations Psychosocial Deprivation SCDO:0000940 A generic term for the treatment of mental illness or emotional disturbances primarily by verbal or nonverbal communication. http://purl.bioontology.org/ontology/MESH/D011613 Sufficient SCDO:0000940 MESH:D011613 Logotherapy Psycho-Therapy Psychotherapy SCDO:0000941 'Describes the type of material the article represents (e.g., Review, Clinical Trial, Retracted Publication, Letter); see the PubMed Publication Types, e.g., review[pt]. Publication Types are arranged hierarchically with more specific terms arranged beneath broader terms. [Curator team: []]' http://bioportal.bioontology.org/ontologies/EDDA_PT?p=classes&conceptid=http%3A%2F%2Fontologies.dbmi.pitt.edu%2Fedda%2FPublicationType.owl%23publication_type obsolete Publication Type true SCDO:0000942 Measurement of the various processes involved in the act of respiration: inspiration, expiration, oxygen and carbon dioxide exchange, lung volume and compliance, etc. Sufficient SCDO:0000942 MESH:D012129 Lung Function Test PFT Respiratory Function Test Pulmonary Function Test SCDO:0000943 An elevation of mean pulmonary arterial systolic pressure (mPASP) (>20 mmHg at rest or >30 mmHg with exercise). The 6th World Symposium on PH reduced it from >25mmHg to >20mmHg for at rest, but did not adjust the definition for PH with exercise. Br J Haematol. 2006 Jul;134(1):109-15. Simonneau et al 2013 J Am Coll Cardiol; Ataga et al. Multifactorial, including chronic thromboembolism, splenectomy, high cardiac output, left-heart disease, and hyperviscosity; the role of an inactivation of nitric oxide by free plasma hemoglobin due to chronic hemolysis is controversial. Few but definitions not specific enough Increased Blood Pressure in Blood Vessels of Lungs Pulmonary Arterial Hypertension Pulmonary hypertension can be secondary to known cardiac, pulmonary, or hepatic disease. If no cause is identifiable, the term primary pulmonary hypertension is used. Pulmonary Hypertension SCDO:0000944 A measurement device, usually attached to the earlobe or fingertip, that measures the oxygen saturation of arterial blood. This consists of 2 parts, the "pulse oximeter monitor" and the "pulse oximeter probe". Perhaps can be included as sub-classes or siblings? See "Pulse Oximetry (Rest)" in PhenX. http://purl.obolibrary.org/obo/ERO_0000876 Sufficient SCDO:0000944 ERO:0000876 Blood Oxygen Monitor Oxygen Monitor Pulse Oximeter SCDO:0000945 The application of pulse oximetry to measure a patient's saturation of oxyhemoglobin when the patient is at rest. Suggest update to description in PhenX Suggest inclusion of term below "Pulse Oximetry" in the CMO. PhenX protocol: Pulse Oximetry (Rest) #91102 Suggest update to description phenX:91102 Pulse Oximetry (Rest) SCDO:0000947 The systemic measurement of the quality of health care that includes a broad set of perfomance measures such as the quality of services and the outcomes analysis for particular diseases and conditions, mortality and morbidity, patient safety, data on maternal and child health, as well as evaluation of quality of diagnosis, care accessibility, implementation of proven evidence-based practices, quality of reporting systems for errors and adverse events, reliability and accessibility of health and health care-related information, and health care organizations infrastructure. Suggest update to description in EDDA (replace "excessability" with "accessibility". Suggest update to description EDDA:health_care_quality_assessment Health Care Quality Assessment Quality of Health Care Assessment Quality of Care Measure SCDO:0000948 The levels of excellence which characterize the health service or health care provided based on accepted standards of quality. http://purl.bioontology.org/ontology/MESH/D011787 Sufficient SCDO:0000948 MESH:D011787 Health Care Quality Healthcare Quality Quality of Healthcare Quality of Health Care SCDO:0000950 The subjective measurement of an individual's sense of well-being and ability to enjoy life, and the levels of excellence which characterize the health service or health care provided to individuals based on accepted standards of quality. Request inclusion into relevant ontology. Include the term "Transition from pediatric care" somewhere...see the source provided here. None SCDO Quality of Life and Care SCDO:0000951 A measurement tool that is useful in aiding routine clinical practice with regard to quality of life and/or quality of care. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) Quality of Life and Care Measurement Scales Quality of Life and Care Measure SCDO:0000952 A questionnaire to assess the physical, emotional, and social impact of chronic conditions, such as sickle cell disease (SCD). Suggest update to label in PhenX. Suggest update to label phenX:820200 Quality of Life in SCD Quality of Life in Sickle Cell Disease Measure SCDO:0000953 A measurement tool with eight potential uses in aiding routine clinical practice. It can be used to prioritise problems, facilitate communication, screen for potential problems, identify preferences, monitor changes or response to treatment, and train new staff. It can also be used in clinical audit and in clinical governance. The first five of these can be used in the clinical encounter, while the last three contribute to training, reviewing care, and improving care in the future. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) Quality of Life Measure SCDO:0000954 Sickle cell symptoms where there is evidence of some relation with quality of life. Probably too specific to be included in other ontologies. None SCDO Quality of Life Related SCD Symptoms and Complications SCDO:0000955 QALYs are used primarily to correct a person's life expectancy based on the levels of health-related quality of life they are predicted to experience throughout the course of their life, or part of it. Multiple countries and cultural groups Self; Proxy All Standard global assessment of health interventions, also used in SCD studies Children and adults no Few but definitions not specific enough QALY Quality-Adjusted Life Year The number of QALYs lived by an individual in one year is simply: QALYs lived in one year = 1 * Q with Q <= 1; where Q is the health-related quality of life weight attached to the relevant year of life. I.e. QALY assumes a utility value (quality of life) of 1 = perfect health and a utility value of 0 = dead: Years of Life x Utility Value = Number of QALYs. E.g. If a person lives in perfect health for one year, that person will have 1 QALY (1 Year of Life x 1 Utility Value = 1 QALY), If a person lives in perfect health but only for half a year, that person will have 0.5 QALYs (0.5 Years of Life x 1 Utility Value = 0.5 QALYs) OR if a person lives for 1 year in a situation with 0.5 utility (half of perfect health), that person will also have 0.5 QALYs (1 Year of Life x 0.5 Utility Value = 0.5 QALYs). In cost-effectiveness evaluations the QALY is used to quantify the effectiveness of, for instance, a new medication versus the current one. In other words, the current standard of care is taken as the baseline, and the QALYs gained from the new (improved) intervention are counted in addition. Quality-Adjusted Life Year (QALY) SCDO:0000957 'Collection of data obtained from voluntary subjects. The information usually takes the form of answers to questions, or suggestions. Predetermined sets of questions used to collect data - clinical data, social status, occupational group, etc. [Curator team: []]' http://bioportal.bioontology.org/ontologies/MESH?p=classes&conceptid=D011795 MESH:D011795 obsolete Questionnaire true SCDO:0000963 Examination of any part of the body for diagnostic purposes by means of x-rays or gamma rays, recording the image on a sensitized surface (such as photographic film). http://purl.bioontology.org/ontology/MESH/D011859 Sufficient SCDO:0000963 MESH:D011859 Imaging by X-Ray X-Ray Radiography SCDO:0000964 The production of an image obtained by cameras that detect the radioactive emissions of an injected radionuclide as it has distributed differentially throughout tissues in the body. The image obtained from a moving detector is called a scan, while the image obtained from a stationary camera device is called a scintiphotograph. http://purl.bioontology.org/ontology/MESH/D011877 Sufficient SCDO:0000964 MESH:D011877 Imaging by Radionuclide Scintigraphy Radionuclide Imaging SCDO:0000965 'A work that reports on a clinical trial that involves at least one test treatment and one control treatment, concurrent enrollment and follow-up of the test- and control-treated groups, and in which the treatments to be administered are selected by a random process, such as the use of a random-numbers table. [Curator team: []]' http://purl.bioontology.org/ontology/MESH/D016449 MESH:D016449 obsolete Randomized Controlled Trial true SCDO:0000966 The Rapid Estimate of Adolescent Literacy or REALM-Teen is a valid, reliable, easy-to-administer tool that will allow health professionals to screen youth in grades 6-12 for below-grade reading. The REALM-Teen is a reading recognition instrument, modeled after the Rapid Estimate of Adult Literacy in Medicine (REALM), the most commonly used tool to screen adults for low literacy in health care settings. The REALM-Teen is a reading recognition instrument which measures an individual's ability to pronounce words in ascending order of difficulty. All test words are commonly used adolescent health terms. Request inclusion into NCIT below "Research or Clinical Assessment Tool". Add these annotation properties: -- has cross-cultural adaptation -- freely available -- has translations Davis TC, Wolf MS, Arnold CL, Byrd RS, Long SW, Springer T, Kennen E, Bocchini JA. (2006). Development and validation of the Rapid Estimate of Adolescent Literacy in Medicine (REALM-Teen): a tool to screen adolescents for below-grade reading in health care settings. Pediatrics 118(6):e1707-14. Self Adolescents with SCD Used in SCD studies Adolescents None Davis TC, Wolf MS, Arnold CL, Byrd RS, Long SW, Springer T, Kennen E, Bocchini JA. (2006). Development and validation of the Rapid Estimate of Adolescent Literacy in Medicine (REALM-Teen): a tool to screen adolescents for below-grade reading in health care settings. Pediatrics 118(6):e1707-14. REALM-Teen Rapid Estimate of Adolescent Literacy in Medicine Rapid Estimate of Adolescent Literacy in Medicine (REALM-Teen) SCDO:0000970 A questionnaire that assesses recovery and recurrence of stroke in children. It is completed by a parent about their child. Suggest update to description in PhenX. http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820702 PhenX protocol: Recovery and Recurrence Questionnaire (RRQ) - Pediatrics #820702 Suggest update to description phenX:820702 RRQ Recovery and Recurrence Questionnaire (RRQ) - Pediatrics Recovery and Recurrence Questionnaire (RRQ) SCDO:0000972 Recurrent episodes of wheezing in persons with SCD who have no co-morbid asthma. Probably too specific to warrant inclusion into anther ontology. Glassberg et al 2014 Curr Opin Pediatr. Knight-Madden et al 2014 Ped Resp Rev Likely related to inflammation of SCD. Other markers of severity of SCD- eg complications of SCD, high LDH. None RWIS Recurrent Wheeze in Sickle Cell Disease SCDO:0000975 The amount of red blood cell derived microparticles in a specific volume of blood. Request inclusion into relevant ontology More info can be taken from the dc:source provided. Perhaps add MeSH term "Cell-Derived Microparticles" as a superclass of this term? None SCDO (Jade Hotchkiss) Cell-Derived Microparticles EMP Level Erythrocyte-Derived Microparticles Level Level of Red Blood Cell Microparticles RBC Microparticles Level Red Blood Cell Derived Microparticles Level Red Blood Cell Microparticles Level SCDO:0000976 Hemoglobin A (HbA) contains two alpha-globin chains and two beta-globin chains. HbA is normally the main adult hemoglobin, representing about 96-98 percent of all hemoglobin. This term represents a decrease in the proportion of HbA below this limit, and can be seen in various forms of thalassemia. Suggest update to description in HPO. http://purl.obolibrary.org/obo/HP_0011905 Suggest update to description HP:0011905 Reduced Hemoglobin A SCDO:0000978 Restoration of human functions to the maximum degree possible in a person or persons suffering from disease or injury. http://purl.bioontology.org/ontology/MESH/D012046 Sufficient SCDO:0000978 MESH:D012046 Habilitation Rehabilitation SCDO:0000979 Reincarnation is the philosophical or religious concept that an aspect of a living being starts a new life in a different physical body or form after each biological death. Request inclusion into relevant ontology http://en.wikipedia.org/wiki/Reincarnation None SCDO Rebirth Transmigration Reincarnation SCDO:0000981 A set of beliefs concerning the nature, cause, and purpose of the universe, especially when considered as the creation of a superhuman agency. It usually involves devotional and ritual observances and often a moral code for the conduct of human affairs. http://purl.bioontology.org/ontology/MESH/D012067 Sufficient SCDO:0000981 MESH:D012067 Religious Beliefs Religious Ethics Religion SCDO:0000983 Therapy for the insufficient cleansing of the BLOOD by the kidneys based on dialysis and including hemodialysis, peritoneal dialysis, and hemodiafiltration. Include types of renal dialysis as sub-classes: -- Peritoneal dialysis -- Hemodialysis -- Pediatric dialysis? -- Hemofiltration -- Hemodiafiltration http://purl.bioontology.org/ontology/MESH/D006435 Sufficient SCDO:0000983 MESH:D006435 Dialyses, Renal Extracorporeal Dialyses Extracorporeal Dialysis Haemodialysis Hemodialyses Renal Dialyses Renal Dialysis SCDO:0000984 Inadequate blood flow to one or both kidneys, or nephrons, usually due to functional constriction or actual obstruction of blood vessels. Suggest update to description in Mammalian Phenotype ontology. Provide source for additional info. Loss of adequate blood flow may be due to obstruction of blood vessels - large or small or due to low flow states such as prolonged hypotension. Usually associated with kidney injury as noted by decrease in urine output and/or elevation in serum creatinine. Suggest update to description MP:0011758 Kidney Ischaemia Kidney Ischemia Nephric Ischaemia Nephric Ischemia Renal Ischaemia Renal Ischemia SCDO:0000985 The transference of a kidney from one human or animal to another. http://purl.bioontology.org/ontology/MESH/D016030 Sufficient SCDO:0000985 MESH:D016030 Kidney Grafting Kidney Transplant Kidney Transplantation Kidney Transplantations Renal Transplantation Renal Transplantations Renal Transplant SCDO:0000986 Acidosis owing to malfunction of the kidney tubules with accumulation of metabolic acids and hyperchloremia. Suggest update to description in HPO. Provide source for additional info. Has multiple types - Type 1 (Distal RTA), Type 2 (Proximal RTA), Type 4 (Hyperkalemic RTA). Sickle cell disease may demonstrate a voltage dependent Type 1 RTA. Defects in the kidneys in reabsorption of bicarbonate (HCO3), the excretion of hydrogen ions (H+), or both. A relatively normal GFR and a metabolic acidosis accompanied by hyperchloremia and a normal plasma anion gap. Suggest update to description HP:0001947 Accumulation of Acid in Body Due to Kidney Problem RTA Renal Tubular Acidosis SCDO:0000987 A questionnaire to assess either male or females' pregnancy history. Females are asked about the number of pregnancies, description of pregnancies and smoking during pregnancy. Males are asked whether they have ever fathered a pregnancy and, if so, the description of the pregnancy. Suggest update to labels of as we have done. We are using "Reproductive History" below Personal Attribute. Also suggest update to description as we have done. Suggest update to label and description phenX:101300 Reproductive History Diagnostic Instrument SCDO:0000988 'Anatomical system that has as its parts the organs concerned with reproduction. [Curator team: []]' http://purl.obolibrary.org/obo/UBERON_0000990 UBERON:0000990 deprecated Reproductive System true SCDO:0000990 'Systematic investigation into a subject in order to discover facts, establish or revise a theory, or develop a plan of action based on the facts discovered. [Curator team: []]' Consider other sub-classes of this in NCIT. http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C15429 NCIT:C15429 obsolete Research Activity true SCDO:0000993 The number of times an organism breathes with the lungs (respiration) per unit time, usually per minute. Sufficient SCDO:0000993 MESH:D056152 Breathing Frequency Pulmonary Ventilation Rate Respiration Rate Respiratory Rate SCDO:0000994 Lungs and respiratory system of the body. Pulmonary System deprecated Respiratory System true SCDO:0001000 Root of all terms in the Sickle Cell Disease Ontology, an effort of unambiguously describing all concepts and unifying up-to-date knowledge in sickle cell disease. None SCDO (Gaston K. Mazandu) Sickle Cell Disease Ontology SCDO SCDO:0001002 PCR-restriction fragment length polymorphism (RFLP)-based analysis, also known as cleaved amplified polymorphic sequence (CAPS), is a popular technique for genetic analysis. It has been applied for the detection of intraspecies as well as interspecies variation. There exist several techniques that are related with PCR-RFLP and also involve gel electrophoresis including techniques for DNA fingerprinting and expression profiling. Request inclusion into relevant ontology. Henrik Berg Rasmussen (April 4th 2012). Restriction Fragment Length Polymorphism Analysis of PCR-Amplified Fragments (PCR-RFLP) and Gel Electrophoresis - Valuable Tool for Genotyping and Genetic Fingerprinting, Gel Electrophoresis Sameh Magdeldin, IntechOpen, DOI: 10.5772/37724. Available from: https://www.intechopen.com/books/gel-electrophoresis-principles-and-basics/restriction-fragment-length-polymorphism-analysis-of-pcr-amplified-fragments-pcr-rflp-and-related-te Few but definitions not freely available PCR-RFLP Restriction Fragment Length Polymorphism - Polymerase Chain Reaction Restriction Fragment Length Polymorphism PCR SCDO:0001004 The number of reticulocytes per unit volume of blood. The values are expressed as a percentage of the erythrocyte count or in the form of an index ("corrected reticulocyte index"), which attempts to account for the number of circulating erythrocytes. PhenX protocol: Reticulocyte Count #810601 Sufficient SCDO:0001004 MESH:D017701 Reticulocyte Number Reticulocyte Count SCDO:0001005 A reticulocyte count that was performed with an electronic haematology analyzer. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) Reticulocyte Count by Hematology Analyzer SCDO:0001006 A reticulocyte count that was performed with microscopy. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) Reticulocyte Count by Microsocopy SCDO:0001007 A procedure that uses intense cold to induce a chorioretinal scar and to destroy retinal or choroidal tissue. Request inclusion into relevant ontology http://www.surgeryencyclopedia.com/Pa-St/Retinal-Cryopexy.html None Retinal Cryotherapy Retinal Cryopexy SCDO:0001008 Separation of the retina from the choroid and eye wall due to holes in the retina and traction on the retina by vitreous bands and condensed preretinal membranes (usually as sequelae of proliferative sickle retinopathy). Retinal detachment is the most severe complication (Stage V) of proliferative sickle retinopathy. We provided a more SCD specific description than the generic descriptions provided in existing ontologies. Ballas et al 2010 Am J Hematol Not relevant to context of sickle cell Retinal Detachment SCDO:0001010 Studies used to test etiologic hypotheses in which inferences about an exposure to putative causal factors are derived from data relating to characteristics of persons under study or to events or experiences in their past. The essential feature is that some of the persons under study have the disease or outcome of interest and their characteristics are compared with those of unaffected persons. http://purl.bioontology.org/ontology/MESH/D012189 Sufficient SCDO:0001010 MESH:D012189 Retrospective Study Retrospective Studies SCDO:0001017 An open swath of land that has few homes or other buildings, and not very many people. Request inclusion into relevant ontology None Rural Rural Area Rural Setting Rural Location SCDO:0001019 Round or oval-shaped intraretinal accumulation of erythrocytes that may be up to 2 mm in diameter. This small intraretinal hematoma is initially red and becomes salmon colored with time. Request inclusion into relevant ontology. Ballas et al 2010 Am J Hematol None Salmon Patch Hemorrhages Salmon Patch Hemorrhage SCDO:0001020 Studies in which a number of subjects are selected from all subjects in a defined population. Conclusions based on sample results may be attributed only to the population sampled. http://purl.bioontology.org/ontology/MESH/D012494 Sufficient SCDO:0001020 MESH:D012494 Probability Sample Probability Samples Sampling Study Sampling Studies SCDO:0001023 Pain resulting from the presence of Sickle Cell Disease (SCD). Such pain can be acute, chronic or a mixture of the two. Request inclusion into relevant ontology None SCDO Okpala I., Tawil A. Management of pain in sickle-cell disease. Journal of the Royal Society of Medicine. 2002;95(9):456-458. doi: 10.1258/jrsm.95.9.456 SCD Pain SCD-Related Pain SCD Related Pain SCDO:0001025 An operation for retinal detachment which reduces the size of the globe by indenting the sclera so that it approximates the retina. http://purl.bioontology.org/ontology/MESH/D012591 Sufficient SCDO:0001025 MESH:D012591 Scleral Buckle Surgery Scleral Bucklings Scleral Buckling SCDO:0001027 Specialized healthcare delivered as a follow-up or referral from a primary care provider. http://purl.bioontology.org/ontology/MESH/D063127 Sufficient SCDO:0001027 MESH:D063127 Secondary Care Secondary Health Care Secondary Healthcare SCDO:0001029 Usual level of physical activity that is less than 30 minutes of moderate-intensity activity on most days of the week. http://purl.bioontology.org/ontology/MESH/D057185 Sufficient SCDO:0001029 MESH:D057185 Sedentary Lifestyle SCDO:0001034 Caring for self when ill or positive actions and adopting behaviors to prevent illness. http://purl.bioontology.org/ontology/MESH/D012648 Sufficient SCDO:0001034 MESH:D012648 Self Management Self-Care Self-Management Self Care SCDO:0001035 Cognitive mechanism based on expectations or beliefs about one's ability to perform actions necessary to produce a given effect. Sufficient SCDO:0001035 MESH:D020377 Self-Concept Self Efficacy SCDO:0001037 The weight in kilograms or pounds as reported by the participant. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) Self-Reported Weight SCDO:0001041 Epidemiologic studies based on the detection through serological testing of characteristic change in the serum level of specific antibodies. Latent subclinical infections and carrier states can thus be detected in addition to clinically overt cases. http://purl.bioontology.org/ontology/MESH/D016036 Sufficient SCDO:0001041 MESH:D016036 Seroprevalences Seroepidemiologic Studies SCDO:0001043 The amount of the HDL cholesterol, the small lipoprotein:cholesterol complex that transports cholesterol out of the arteries and to the liver for reprocessing or excretion, in a specified volume of serum. Request inclusion into relevant ontology Few but definitions not freely available SCDO (Jade Hotchkiss) Blood HDL Cholesterol Amount Blood High Density Lipoprotein Cholesterol Amount Circulating HDL Cholesterol Amount Circulating HDL Cholesterol Level HDL Cholesterol Level HDL Level Serum HDL Cholesterol Level SCDO:0001044 A 36-item instrument for measuring health status and outcomes via patient self-report. It is designed for use in surveys of general and specific populations, health policy evaluations, and clinical practice and research. The SF-36v2 measures the following eight health concepts, which are relevant across age, disease, and treatment groups: physical functioning, role limitations due to physical health problems, bodily pain, general health, vitality (energy/fatigue), social functioning, role limitations due to emotional problems, and mental health (psychological distress and psychological well-being). Both standard (4-week) and acute (1-week) recall versions are available. The survey's standardized scoring system yields a profile of eight health scores and two summary measures (physical and mental health) and a self-evaluated change in health status. Add these annotation properties: -- has cross-cultural adaptation -- freely available -- has translations Suggest update to label in PhenX (from "Physical, Social, and Mental Health Functioning (SF-36V2)") PhenX protocol: #191201 Self Healthy people; Clinic patients Demonstrated validity with SCD populations; multiple publications using the measure in SCD; very widely used with healthy populations and those with chronic conditions Adults 18 years and older Suggest update to label SF-36v2 Health Survey SCDO:0001047 A measure of stigma among adults living with Sickle Cell disease. Focus on; depressive symptoms, pain, assertive communication, satisfaction with pain management experience, and health-related stigma. Request inclusion into NCIT below "Research or Clinical Assessment Tool". Add these annotation properties: -- has respondents -- has target population -- selection criteria met -- validated for age ranges -- has cross-cultural adaptation -- freely available -- has translations Jenerette C, Brewer CA, Crandell J, Ataga KI. Preliminary validity and reliability of the Sickle Cell Disease Health-Related Stigma Scale.Issues Ment Health Nurs.2012 Jun;33(6):363-9. None Jenerette C, Brewer CA, Crandell J, Ataga KI. Preliminary validity and reliability of the Sickle Cell Disease Health-Related Stigma Scale.Issues Ment Health Nurs.2012 Jun;33(6):363-9. SCD-HRSS Sickle Cell Disease Health-Related Stigma Scale Sickle Cell Disease Health-Related Stigma Scale (SCD-HRSS) SCDO:0001048 The SCPBI-Y is a brief clinical interview designed to assess pain burden for children and adolescents with SCD. Request inclusion into NCIT below "Research or Clinical Assessment Tool". Add these annotation properties: -- has respondents -- has target population -- selection criteria met -- validated for age ranges -- has cross-cultural adaptation -- freely available -- has translations Zempsky WT, O'Hara EA, Santanelli JP, Palermo TM, New T, Smith-Whitley K, Casella JF. Validation of the sickle cell disease pain burden interview-youth. J Pain. 2013 Sep;14(9):975-82. None SCPBI-Y Sickle Cell Disease Pain Burden Interview - Youth SCDO:0001049 Sickle cell tests are used to help diagnose sickle cell anemia (also called sickle cell disease) and to identify those who may have sickle cell trait. Sickle cell anemia is an inherited disorder that leads to the production of an abnormal hemoglobin called hemoglobin S (Hb S or Hgb S). Sickle cell tests determine the presence and relative amount of hemoglobin S in a blood sample. Request inclusion into relevant ontology https://labtestsonline.org/tests/sickle-cell-tests Few but definitions not freely available Screening for Sickle Cell Disease Sickle Cell Disease Screening Test SCDO:0001050 A nine-item self-administered questionnaire that measures disease-specific perceptions of the ability to manage day-to-day issues resulting from sickle cell disease (SCD). Items are scores according to a five-point scale ranging from 1 - Not sure at all to 5 - Very sure. Responses from individual items are summed to give an overall score with higher scores indicating greater self-efficacy. Suggest update to label in PhenX as we have done. PhenX protocol: Self-efficacy in Sickle Cell Disease #820401 Self Clinic Patients (Adults with SCD) Self-efficacy, or one’s perceptions that they can exercise control over their behaviors and environment, may play an important role in determining the ability to adjust to chronic conditions such as sickle cell disease (SCD). 18 and older Suggest update to label Scale of Self-efficacy in Sickle Cell Disease Sickle Cell Disease Self-Efficacy Scale SCDO:0001051 A variant form of sickle cell disease that results from inheriting the sickle mutation in combination with another beta-globin gene mutation. These hemoglobinopathies may have different clinical severity compared to the homozygous form of sickle cell disease (HbSS). Request inclusion into relevant ontology http://www.uptodate.com/contents/overview-of-variant-sickle-cell-syndromes None SCD Variant Sickle Cell Disease Variant Variant Sickle Cell Syndromes Variant Sickle Cell Syndrome SCDO:0001052 A form of therapy that employs a coordinated and interdisciplinary approach for easing the suffering and improving the quality of life of those experiencing sickle cell related pain. Request inclusion into MESH below "Pain Management". http://purl.bioontology.org/ontology/MESH/D059408 None SCDO Sickle Cell Pain Managements Sickle Cell Pain Management SCDO:0001053 Pain lasting at least two hours that requires an unscheduled emergency room visit or hospitalization or that disrupts daily activities. Could be categorised as a phenotype "Finding". Request inclusion into relevant ontology None SCDO http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=830101 Pain Episode Painful Crisis Painful Event Sickle Cell Acute Pain Episode Sickle Cell Pain Episode Sickle Cell Painful Event SCDO:0001054 A cancer that is almost exclusively associated with sickle cell trait and/or sickle cell disease. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) Sickle Cell Associated Cancer Sickle Cell Related Cancer SCDO:0001055 The condition of being heterozygous for hemoglobin S. http://purl.bioontology.org/ontology/MESH/D012805 Sufficient SCDO:0001055 MESH:D012805 AS Genotype Haemoglobin Genotype AS Hemoglobin Genotype AS Sickle Cell Trait SCDO:0001056 A mild form of sickle cell thalassemia characterized by the presence of hemoglobin S and a reduced amount of hemoglobin A in the red blood cells. It is characterized by the presence of small red blood cells and mild anemia. Suggest update to label in NCIT from "Sickle Beta Plus Thalassemia" to "Sickle Beta Minus Thalassemia" http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C98837 Suggest update to label NCIT:C98837 S beta-minus Sickle B- Thalassemia Sickle Beta Minus Thalassemia Sickle Cell Disease-S Beta Minus Thalassemia Sickle Cell-B- Thalassemia Sickle Cell-Beta Minus Thalassemia Sickle Cell Disease-S Beta Minus Thalassemia SCDO:0001059 One of the sickle cell disorders characterized by the presence of both hemoglobin S and hemoglobin C. It is similar to, but less severe than sickle cell anemia. http://purl.bioontology.org/ontology/MESH/D006450 Sufficient SCDO:0001059 MESH:D006450 Hb SC-disease Hemoglobin S / Hemoglobin C Disease Hemoglobin SC Disease SC Disease Sickle Cell Disease SC Sickle Cell Hemoglobin C Disease Sickle Cell-Haemoglobin C Disease Sickle Cell-Hemoglobin C Disease Sickle-Cell/Hb-C Disease Sickle Cell Disease-SC SCDO:0001061 A rare compound heterozygous hemoglobinopathy characterised by the presence of two beta globin gene variants: that of hemoglobin S (beta-6(GAG-->GTG)) and that of hemoglobin D-Punjab (beta-121(GAA-->CAA)). Request inclusion into relevant ontology. Perhaps as sub-class of "Sickle Cell-Hemoglobin D Disease" in the NCIT. Rahimah Ahmad*, Syahira Lazira Omar*, Siti Hida H M Arif*, Faidatul Syazlin A Hamid*, Nur Aisyah Aziz*, Nik Hafidzah N Mustapha**, Zubaidah Zakaria*Haemoglobin Sickle D Punjab: - A Case Report. Med J Malaysia. 2014. Vol 69 No 1. Few but definitions not freely available Haemoglobin S/D-Punjab Hemoglobin S/D-Punjab Sickle Cell-Haemoglobin D-Punjab Sickle Cell-Hemoglobin D-Punjab Disease Sickle Cell Disease-S/D-Punjab SCDO:0001062 A variant of sickle cell disease due to heterozygosity for hemoglobin S and hemoglobin E mutations, which can cause mild hemolytic anemia. Suggest update to description of "Sickle Cell-Hemoglobin D Disease" in the NCIT. http://newbornscreeningcodes.nlm.nih.gov/nb/sc/condition/Hb-F-S-E Few but definitions not specific enough Hb SE-Disease Hemoglobin SE Disease Hemoglobin SE-Disease Sickle Cell Disease SE Sickle Cell-Haemoglobin E Disease Sickle Cell-Hemoglobin E Disease Sickle Cell Disease-SE SCDO:0001063 Sickle cell-Hb Lepore Boston syndrome is a type of sickle cell disease that differs from homozygous sickle cell disease where both parents carry sickle hemoglobin. In this variant one parent has the sickle cell hemoglobin the second parent has Hb Lepore Boston, the only one of the three Hb Lepore variants described in association with HbS. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) SCD-S/Lepore Boston Sickle Cell Disease-S/Lepore Sickle Cell-Hb Lepore Boston Syndrome Sickle Cell-Hemoglobin Lepore Boston Syndrome Hb Lepore Washington, also known as Hb Lepore Boston or Hb Lepore Washington-Boston; most common in Italians from Southern Italy. Sickle Cell Disease-S/Lepore Boston SCDO:0001064 One of the sickle cell disorders characterized by the presence of both hemoglobin S and hemoglobin O-Arab. It can cause anemia, repeated infections, and periodic episodes of pain and organ damage. Request inclusion into relevant ontology http://newbornscreeningcodes.nlm.nih.gov/nb/sc/condition/Hb-F-S-O-Arab Few but definitions not freely available Hb F,S,O-Arab Hb S O-Arab disease Hb S,O-Arab Hemoglobin S O-Arab Disease SO(Arab) disease Sickle Cell-Haemoglobin O-Arab Disease Sickle Cell-Hemoglobin O-Arab Disease Sickle Cell Disease-S/O-Arab SCDO:0001065 'A variant of sickle cell disease in which individuals have atypical hemoglobin molecules called hemoglobin S together with another form of abnormal hemoglobin, other than hemoglobin C,D,E and O-Arab. [Curator team: []]' http://newbornscreeningcodes.nlm.nih.gov/nb/sc/condition/Hb-F-S-and-other-than-A-C-D-E-O-Arab Hb S Other than A,C,D,E,O-Arab obsolete Sickle Cell-Hemoglobin Other than A,C,D,E,O-Arab true SCDO:0001067 Retinal changes of sickle cell disease that can be either proliferative or non-proliferative. In both cases, the changes are caused by erythrostasis secondary to sickling. Request inclusion into HPO below "Retinopathy". Use the scielo source to add info on diagnosis and treatment. Bonanomi et al 2013 Arq Bras Oftalmol Few but definitions not freely available Retinopathy due to SCD Sickle Cell Retinopathy Sickle Retinopathy SCDO:0001068 A qualitative screening test for sickling haemoglobins, especially HbS. In the SCT, sodium metabisulfite or sodium dithionate is used to desolubilise haemoglobin S to the crystallised deoxygenated form, which causes the abnormal RBCs to sickle, as detected by light microscopy. In SNOMED CT this term seems to be both "Sickle cell identification, slide method" and "Sickling Test". Request they merge these terms? Segen's Medical Dictionary. © 2012 Farlex, Inc. Few but definitions not freely available. Sickle Cell Identification, Slide Method Sickling Test SCDO:0001069 A generic measure used to evaluate the impact of SCD on both physical and emotional functioning of an affected person. SIP is designed to measure perceived health status and to be used as an outcome measure for evaluation, program planning, and policy formation related to health care. It is designed in such a way as to reflect sensitivity to changes and/or differences in health status and to be applicable across a broad range of types and severities of the SCD illness, as well as different demographic and cultural groups. Too specific to SCD to be included in other ontologies. These annotation properties still required: -- has respondents -- has target population -- selection criteria met -- validated for age ranges -- has cross-cultural adaptation -- freely available -- has translations http://link.springer.com/referenceworkentry/10.1007%2F978-0-387-79948-3_1833 http://qol.thoracic.org/sections/instruments/pt/pages/sick.html Few but definitions not specific enough SCDO Bergner M., Bobbitt R.A., Carter W.B. and Gilson B.S. (1981). The Sickness Impact Profile: development and final revision of a health status measure. Medical Care 19,787-805. SIP Sickness Impact Profile Sickness Impact Profile (SIP) SCDO:0001070 'The bodily system consisting of the skin and its associated structures, such as the hair, nails, sweat glands, and sebaceous glands. [Curator team: []]' integumentary system. (n.d.) The American Heritage Medical Dictionary. (2007). Retrieved December 14 2016 Dermatologic System Integumentary System deprecated Skin true SCDO:0001073 An abnormal change in skin color, appearance, or texture. Suggest update to description in HPO. Suggest update to description HP:0000988 Exanthem Skin Rash SCDO:0001075 An intrinsic sleep disorder characterized by breathing abnormalities. http://purl.obolibrary.org/obo/NBO_0000494 Suffcient NBO:0000494 SBD Sleep Breathing Disorder SCDO:0001076 An interviewer-administered questionnaire which captures routine sleep schedule, sleep deprivation, morningness-eveningness, insomnia, narcolepsy, cataplexy and associated distress. Suggest update to label in PhenX (from "Suggest update to label") as we have done. PhenX protocol: Sleep Disorders Screener #121001 Suggest update to label phenX:121001 National Institute of Mental Health (NIMH) Sleep Patterns and Problems Instrument Sleep Disorders Screener - Adult SCDO:0001077 A microscope with a light source that can be projected into a linear beam. It allows cross-sectional viewing of the aqueous humor; conjuncteiva; cornea; eyelids; iris; and lens of the eye. http://purl.bioontology.org/ontology/MESH/D066167 Sufficient SCDO:0001077 MESH:D066167 Slit Lamp SCDO:0001079 Inhaling and exhaling the smoke of burning tobacco (Cigar, Cigarette, Hookah, Pipe, Smoking, Waterpipe). http://purl.bioontology.org/ontology/MESH/D012907 Sufficient SCDO:0001079 MESH:D012907 Smoking SCDO:0001080 Discontinuing the habit of smoking. http://purl.bioontology.org/ontology/MESH/D016540 Sufficient SCDO:0001080 MESH:D016540 Quit Smoking Smoking Cessation SCDO:0001082 The aggregate of social and cultural institutions, forms, patterns, and processes that influence the life of an individual or community. http://purl.bioontology.org/ontology/MESH/D012931 Sufficient SCDO:0001082 MESH:D012931 Social Ecology Social Environment SCDO:0001083 Social functioning defines an individual's interactions with their environment and the ability to fulfill their role within such environments as work, social activities, and relationships with partners and family. Request inclusion into relevant ontology Include terms for social relationships; social activities? Compr Psychiatry. 2000 Jan-Feb;41(1):63-9. Assessment of social functioning in depression. Few but definitions not freely available PROMIS Domain Frameworks/Definitions nih.promis.org Social Functioning SCDO:0001084 The separation of individuals or groups resulting in the lack of or minimizing of social contact and/or communication. This separation may be accomplished by physical separation, by social barriers and by psychological mechanisms. In the latter, there may be interaction but no real communication. http://purl.bioontology.org/ontology/MESH/D012934 Sufficient SCDO:0001084 MESH:D012934 Social Isolations Social Isolation SCDO:0001085 A role that is ascribed to individuals in a community. http://semanticscience.org/resource/SIO_000676 Sufficient SCDO:0001085 SIO:000676 Social Function Social Role SCDO:0001086 An extent/ degree to which an individual fulfills the expectations of his/her social role. Request inclusion into relevant ontology None SCDO Social Role Fulfillment SCDO:0001087 The personal set of abilities required to successfully interact and communicate with others, both verbally and non-verbally through gestures, body language and personal appearance. http://purl.bioontology.org/ontology/MESH/D066107 Sufficient SCDO:0001087 MESH:D066107 Interpersonal Skill Social Ability Social Competence Social Skills Social Skill SCDO:0001088 Support systems that provide assistance and encouragement to individuals with physical or emotional disabilities in order that they may better cope. Informal social support is usually provided by friends, relatives, or peers, while formal assistance is provided by churches, groups, etc. http://purl.bioontology.org/ontology/MESH/D012944 Sufficient SCDO:0001088 MESH:D012944 Psychosocial Support System Social Network Social Support SCDO:0001089 Abstract standards or empirical variables in social life which are believed to be important and/or desirable. http://purl.bioontology.org/ontology/MESH/D012945 Sufficient SCDO:0001089 MESH:D012945 Value Orientation Value Orientations Social Values SCDO:0001090 Social and economic factors that characterize the individual or group within the social structure. Maybe include some sub-classes of this term in MESH? There would be overlap with terms in QOL, so would need to work around that. http://purl.bioontology.org/ontology/MESH/D012959 Sufficient SCDO:0001090 MESH:D012959 Socioeconomic Factors SCDO:0001091 The combination of one's social class and income level. Includes socioeconomic differences between individuals or groups. http://bioportal.bioontology.org/ontologies/APAONTO/?p=classes&conceptid=http%3A%2F%2Fontology.apa.org%2Fapaonto%2FtermsonlyOUT%2520%285%29.owl%23Socioeconomic_Status Sufficient SCDO:0001091 APAONTO:Socioeconomic_Status Socioeconomic Status SCDO:0001092 A basic first line test that looks for the presence of abnormal Hemoglobin S in a blood sample. Sodium metabisulfite is added to the blood sample which causes Hb S polymerisation and sickling of red blood cells if Hb S is present. A positive result means that a person has either Sickle Cell Disease or Sickle Cell Trait. Confirmatory tests are needed to distinguish which form of SCD the patient has. In SNOMED CT this term is "Hemoglobin S Solubility Test" Commonly used tests include hemoglobin electrophoresis, isoelectric focusing (IEF), high performance liquid chromatography (HPLC), and DNA analysis. Few but definitions not freely available. SCDO (Clair Ingram) Hemoglobin S Solubility Test Solubility Test SCDO:0001097 Instruments for measuring arterial blood pressure consisting of an inflatable cuff, inflating bulb, and a gauge showing the blood pressure. http://purl.bioontology.org/ontology/MESH/D019722 Sufficient SCDO:0001097 MESH:D019722 Sphygmomanometer SCDO:0001098 Sensitivity or attachment to religious values, or to things of the spirit as opposed to material or worldly interests. http://purl.bioontology.org/ontology/MESH/D029181 Sufficient SCDO:0001098 MESH:D029181 Spiritual Beliefs Spiritualities Spirituality SCDO:0001099 A spirometer is an apparatus for measuring the volume of air inspired and expired by the lungs. It is a precision differential pressure transducer for the measurements of respiration flow rates. The spirometer records the amount of air and the rate of air that is breathed in and out over a specified period of time. http://purl.obolibrary.org/obo/ERO_0000452 Sufficient SCDO:0001099 ERO:0000452 Spirometer SCDO:0001105 A form of nephrotic syndrome that does not respond to treatment with steroid medication after 8 weeks, specifically in children. Suggest update to description in HPO Provide source for additional info. May represent underlying focal segmental glomerulosclerosis, minimal change disease, or other underlying cause. Can be subseqeunt to known mutations. Persistence of nephrotic syndrome despite appropriate treatment with corticosteroids. Suggest update to description HP:0012588 Steroid-Resistant Nephrotic Syndrome SCDO:0001107 A perceived attribute that is deeply discrediting and is considered to be a violation of social norms. http://purl.bioontology.org/ontology/MESH/D057545 Sufficient SCDO:0001107 MESH:D057545 Social Stigma Social Stigmas Stigmas Stigma SCDO:0001108 An oversimplified perception or conception, especially or persons, social groups, etc. http://purl.bioontology.org/ontology/MESH/D013240 Sufficient SCDO:0001108 MESH:D013240 Stereotyping Stigmatization SCDO:0001111 A group of pathological conditions characterized by sudden loss of neurological function due to brain ischemia or intracranial hemorrhages. Stroke is classified by the type of tissue necrosis, such as the anatomic location, vasculature involved, etiology, age of the affected individual, and hemorrhagic vs. non-hemorrhagic nature. Types of stroke relevant to SCD to be added as children of this class. http://purl.bioontology.org/ontology/MESH/D020521 Sufficient SCDO:0001111 MESH:D020521 Brain Vascular Accident CVA Cerebral Infarction Cerebral Vascular Event Cerebrovascular Accident Cerebrovascular Stroke Stroke SCDO:0001112 This measure is a physical assessment to determine neurological deficits due to a stroke. Suggest update to label in PhenX This measure is used to describe the consequences of a stroke and to monitor the effects of treatment and recovery. Suggest update to label phenX:820800 Stroke Impact/Outcome Measure Stroke Outcome Measure Stroke Impact Measure SCDO:0001113 This questionnaire includes 59 proxy- or self-report items in 8 domains that assess multidimensional stroke outcomes in adults. Suggest update to description in PhenX. http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820701 PhenX protocol: Stroke Impact Scale (SIS) - Adults #820701 Suggest update to description phenX:820701 Stroke Impact Scale (SIS) - Adults Stroke Impact Scale (SIS) SCDO:0001114 A clinical test to measure the blood flow velocities in intracranial arteries. Elevated intracranial arterial blood flow rates are indicative of expanding vessel lesions and a subsequent increased risk of stroke. Include below "Cerebral Flow Test"? -- Include below "Vascular Endothelial Function Test"? Sufficient SCDO:0001114 phenX:821001 Stroke Risk Test in Children with Sickle Cell Disease SCDO:0001117 The occurrence of multiple self-limited episodes of unwanted, often painful erections lasting <4 hours. Request inclusion into relevant ontology, perhaps below "Priapism" in MESH. Evidence-Based Management of Sickle Cell Disease, Expert Panel Report, 2014 Few but definitions not freely available SCDO Recurrent Priapism Stuttering Priapism SCDO:0001120 Assessment with the goal to obtain a relevant drug and alcohol history and perform a physical examination in order to establish whether there is a diagnosis of a substance use disorder. Few but definitions not specific enough SCDO If substance use disorder diagnosed, the patient’s readiness to change should be categorized and information from the assessment should be used to formulate a management plan based on the individual’s needs. Substance Use History SCDO:0001121 An indication of whether the respondent has ever used a drug during his or her entire life. Request inclusion into relevant ontology Not relevant to context of sickle cell SCDO (Jade Hotchkiss) Substances - Lifetime Use SCDO:0001122 Frequent thinking about or preoccupation with killing oneself. Suggest update to description in HPO (correct typo in "oneself") Suggest update to description HP:0031589 Suicidal Ideation Suicidal Thoughts SCDO:0001123 Organizations which provide an environment encouraging social interactions through group activities or individual relationships especially for the purpose of rehabilitating or supporting patients, individuals with common health problems, or the elderly. They include therapeutic social clubs. http://purl.bioontology.org/ontology/MESH/D012657 Sufficient SCDO:0001123 MESH:D012657 Self Help Group Self-Help Group Self-Help Groups Therapeutic Social Club Support Group SCDO:0001129 Measures aimed at providing appropriate supportive and rehabilitative services to minimize morbidity and maximize quality of life after a long-term disease or injury is present. http://purl.bioontology.org/ontology/MESH/D055512 Sufficient SCDO:0001129 MESH:D055512 Supportive Therapy Tertiary Prevention Supportive Therapeutics SCDO:0001132 A computerized test for the assessment of visual attention problems in individuals ages 8 years old and older. Suggest update to label in PhenX as we have done. http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=821201 PhenX protocol: Sustained and Selective Attention #821201 Suggest update to label phenX:821201 Conners CPT 3 Conners Continuous Performance Test 3rd Edition Conners Continuous Performance Test 3rd Edition (Conners CPT 3) Sustained and Selective Attention Diagnostic Instrument SCDO:0001133 Therapeutics that ease the symptoms without addressing the basic cause of the disease. Request inclusion into relevant ontology http://www.medicinenet.com/script/main/art.asp?articlekey=10701 None SCDO (Jade Hotchkiss) Symptomatic Treatment Symptomatic Therapeutics SCDO:0001135 Refers to a worsening, over a short period of time, of the symptoms and signs of SCD; usually associated with pain and/or shortage of blood (anaemia). Can be suspected in a person with sickle cell disease who presents with a sudden onset of pain, infection, anemia or other symptoms such as stroke or priapism. Acute pain frequently occurs spontaneously, but may be precipitated by infections, skin cooling, dehydration or stress. Request inclusion into relevant ontology This is a difficult one to describe, as I think it can also be referred to as an 'acute painful crisis' (this is not clear from the literature). Have tried to merge descriptions from different sources - please review. Rees, D. C., Olujohungbe, A. D., Parker, N. E., Stephens, A. D., Telfer, P. and Wright, J. (2003), Guidelines for the management of the acute painful crisis in sickle cell disease. British Journal of Haematology, 120: 744-752. doi:10.1046/j.1365-2141.2003.04193.x SCD Management guidelines - Nigeria None SCDO Acute Sickle Cell Crisis SCDO:0001136 'Affecting a number of tissues relating to the entire organism as distinguished from and of its individual parts. [Curator team: []]' http://medical-dictionary.thefreedictionary.com/systemic deprecated Systemic true SCDO:0001140 Care of a highly technical and specialized nature, provided in a medical center, usually one affiliated with a university, for patients with unusually severe, complex, or uncommon health problems. http://purl.bioontology.org/ontology/MESH/D063128 Sufficient SCDO:0001140 MESH:D063128 Tertiary Care Tertiary Health Care Tertiary Healthcare SCDO:0001141 The Test of Functional Health Literacy Assessment (TOFHLA) assesses a patient's level of comprehension of health-related material. It is available in a full-format (a 22-minute test, with 50 reading comprehension items in three passages and 17 numeracy items), an abbreviated format (a 12-minute test, with 36 reading comprehension items in two passages and four numeracy items) and a shortened version (the S-TOFHLA, a 7-minute test, with 36 reading comprehension items in 2 passages.). The passages on the S-TOFHLA use a modified Cloze procedure where every fifth to seventh word is omitted and subjects select the correct word from among a set of four options. The passages contain information about an upper gastrointestinal tract x-ray procedure, and the "Rights and Responsibilities" section from a Medicaid application, and have Gunning-Fox readability indices of fourth and tenth grade, respectively. In early developmental studies, the reading comprehension passages in the S-TOFHLA had a reliability coefficient (Cronbach's alpha) of 0.97 and correlation with the Rapid Estimate of Adult Literacy in Medicine (REALM) of 0.81. Each selection is scored a "1" for correct or a "0" for incorrect and scores are summed over items to create a total score. The 36-point scale of the S-TOFHLA is divided into three categories of functional literacy: inadequate (0-16), adequate (17-22) and functional (23-36). Request inclusion into NCIT below "Research or Clinical Assessment Tool". Still must add these annotation properties: -- has respondents -- has target population -- selection criteria met -- validated for age ranges -- has cross-cultural adaptation -- freely available Parker RM, Baker DW, Williams MV, Nurss JR. The test of functional health literacy in adults: a new instrument for measuring patients' literacy skills. Journal of General Internal Medicine. 1995;10(10):537-41. Spanish None Parker RM, Baker DW, Williams MV, Nurss JR. The test of functional health literacy in adults: a new instrument for measuring patients' literacy skills. Journal of General Internal Medicine. 1995;10(10):537-41. TOFHLA Test of Functional Health Literacy in Adults Test of Functional Health Literacy in Adults (TOFHLA) SCDO:0001146 The Duke Religion Index (DUREL) is a five item scale which measures religiosity in three areas: organizational religiosity (OR), non-organizational religiosity (NOR), and intrinsic religiosity. Two of the questions were derived from large epidemiologic studies and have been shown to have a strong predictive value for many health outcomes. OR has been related to less depression, more social support, better physical health, lower resource utilization, and lower mortality. NOR has been shown to be related to poorer physical health, and greater social support. The other three items were taken from the Hoge 10- item religiosity scale (Hodge et al 1972). The DUREL has high test-retest reliability (intra-class correlation = 0.91), high internal consistency (Cronbach's alpha's = 0.78--0.91). Request inclusion into NCIT below "Research or Clinical Assessment Tool". Also requires these properties: -- has cross-cultural adaptation -- has translations Koenig, HG and Büssing A. (2010). The Duke University Religion Index (DUREL): A Five-Item Measure for Use in Epidemological Studies. Religions, 1, 78-85. Self Adults with SCD Used in at least one SCD study Adults no None Koenig, HG and Büssing A. (2010). The Duke University Religion Index (DUREL): A Five-Item Measure for Use in Epidemological Studies. Religions, 1, 78-85. DUREL The Duke Religion Index The Duke Religion Index (DUREL) SCDO:0001150 A medical device used to prevent and treat medical conditions, or to alleviate pain or injury. Request inclusion into relevant ontology Negligable SCDO Therapeutic Device SCDO:0001151 The washing of a body cavity or surface by flowing water or solution for therapy or diagnosis. http://purl.bioontology.org/ontology/MESH/D007507 Sufficient SCDO:0001151 MESH:D007507 Lavage Lavages Therapeutic Irrigations Therapeutic Irrigation SCDO:0001152 Procedures, agents or devices concerned with the remedial treatment or prevention of diseases. Chemotherapy to be added in this class? If so, would have to be specific types of chemotherapy relevant to the type of therapeutics class. Include as subclasses: -- Prosthesis -- Phototherapy (therapy for Jaundice) -- Risk Reduction? Copy relevant disease modifiers below this. Suggest update to description in MESH Suggest update to description MESH:D013812 Therapy Treatment Therapeutics SCDO:0001158 A mutation named with the blend of insertion and deletion. It refers to a length difference between two alleles where it is unknowable if the difference was originally caused by a sequence insertion or by a sequence deletion. If the number of nucleotides in the insertion/deletion is not divisible by three, and it occurs in a protein coding region, it is also a frameshift mutation. http://purl.bioontology.org/ontology/MESH/D054643 Sufficient SCDO:0001158 MESH:D054643 Insertion-Deletion Mutation Indel Mutation SCDO:0001159 Ending the tobacco habits of smoking, chewing, or snuff use. http://purl.bioontology.org/ontology/MESH/D020340 Sufficient SCDO:0001159 MESH:D020340 Tobacco Cessation Tobacco Use Cessation SCDO:0001164 A person who practices the art of healing using traditional medicine, a system of medicine based on cultural beliefs and practices handed down from generation to generation. The concept includes mystical and magical rituals (spiritual therapies); phytotherapy (plant therapy) and other treatments which may not be explained by modern medicine. Request inclusion into relevant ontology, perhaps MESH. Few but definitions not specific enough SCDO Faith Healer Folk Healer Healer Sangoma Shaman Traditional Healer SCDO:0001165 An interviewer-administered, two-part test that requires the respondent to organize numerical and alphabetical sequences that are randomly distributed on a piece of paper. The protocol includes instructions for correcting mistakes and instructions for scoring based on speed and accuracy. Suggest update to label in PhenX. PhenX protocol: #131101 Suggest update to label phenX:131101 Executive Function - Adult Trail Making Test SCDO:0001166 A non-invasive technique using ultrasound for the measurement of cerebrovascular hemodynamics, particularly cerebral blood flow velocity and cerebral collateral flow. With a high-intensity, low-frequency pulse probe, the intracranial arteries may be studied transtemporally, transorbitally, or from below the foramen magnum. http://purl.bioontology.org/ontology/MESH/D017585 Sufficient SCDO:0001166 MESH:D017585 TCD Transcranial Doppler Ultrasonography, Doppler, Transcranial Transcranial Doppler Ultrasonography SCDO:0001167 The use of specifically placed small electrodes to deliver electrical impulses across the skin to relieve pain. It is used less frequently to produce anesthesia. http://purl.bioontology.org/ontology/MESH/D004561 Sufficient SCDO:0001167 MESH:D004561 Analgesic Cutaneous Electrostimulation Electroanalgesia Electroanalgesias Percutaneous Electrical Nerve Stimulation Percutaneous Electrical Neuromodulations Percutaneous Neuromodulation Therapies Percutaneous Neuromodulation Therapy TENS Transcutaneous Electric Stimulation Transcutaneous Electrical Stimulation Transcutaneous Nerve Stimulation Transdermal Electrostimulation Transcutaneous Electrical Nerve Stimulation SCDO:0001168 Temporary loss of vision in one eye due to a lack of blood flow to the retina. Request inclusion into HP below "Blindness". None SCDO Amaurosis Fugax TMB Temporary Blindness Transient Monocular Blindness SCDO:0001197 'Work consisting of reporting using a method of detecting genetic causes in human traits and genetic factors in behavior using sets of twins. [Curator team: []]' http://purl.bioontology.org/ontology/MESH/D018486 MESH:D018486 obsolete Twin Study true SCDO:0001198 Works about methods of detecting genetic etiology in human traits. The basic premise of twin studies is that monozygotic twins carry identical genes, while zygotic twins are genetically no more similar than two siblings born after separate pregnancies. (Last, J.M., A Dictionary of Epidemiology, 2d ed) http://purl.bioontology.org/ontology/MESH/D018433 Sufficient SCDO:0001198 MESH:D018433 Twin Studies as Topic SCDO:0001200 This gene encodes a UDP-glucuronosyltransferase, an enzyme of the glucuronidation pathway that transforms small lipophilic molecules, such as steroids, bilirubin, hormones, and drugs, into water-soluble, excretable metabolites. This gene is part of a complex locus that encodes several UDP-glucuronosyltransferases. The preferred substrate of this enzyme is bilirubin, although it also has moderate activity with simple phenols, flavones, and C18 steroids. Mutations in this gene result in Crigler-Najjar syndromes types I and II and in Gilbert syndrome. Request inclusion into relevant ontology Few but definitions not freely available GNT1 UDP Glucuronosyltransferase Family 1 Member A1 UGT1 UGT1A1 Gene UGT1A1 SCDO:0001204 The region surrounding a city. Most inhabitants of urban areas have nonagricultural jobs. Urban areas are very developed, meaning there is a density of human structures such as houses, commercial buildings, roads, bridges, and railways. Request inclusion into relevant ontology None Urban Urban Area Urban Environment Urban Setting Urban Location SCDO:0001205 A bioassay to measure urine concentration of albumin, which is produced by the liver and is the most abundant protein in the blood. Label different from source's "Urinary Microalbumin - Assay" PhenX protocol: Urinary Microalbumin Assay #141501 Suggest update to label In the protocol provided, albumin concentration is measured according to a fluorescent immunoassay (FIA). The protocol also lists reference ranges for healthy adults. The criteria for clinically significant proteinuria have been changed from an albumin-creatinine ratio (ACR) of 30 mg/mmol or more to 3 mg/mmol or more. This is because there is evidence that the risk of adverse outcomes is a continuum and starts at an ACR well below 30 mg/mmol. The Sickle Cell Disease Research and Scientific Panel notes that the terms "microalbuminuria" and "macroalbuminuria" have been used clinically to describe different levels of abnormal albumin excretion rate: 30-299 mg/g urine creatinine, and >300 mg/gr urine creatinine, for microalbuminuria and macroalbuminuria, respectively. Recently, a new terminology has been proposed: "low level albuminuria" instead of microalbuminuia, and "high level albuminuria" for macroalbuminuria, since the older terminology could be interpreted as measuring different molecular forms of albumin. Because albuminuria may be affected by non-pathological factors (exercise, menstruation contamination, biological variability, etc.), abnormal values should be confirmed within 1-2 months. Urinary Albumin Test SCDO:0001206 A bioassay to measure urine concentration of creatinine, a muscle metabolite that is filtered out of blood by the kidneys. PhenX protocol: Urinary Creatinine - Assay #141601 Sufficient SCDO:0001206 phenX:141601 Urinary Creatinine Assay Urine Creatinine Analysis Urinary Creatinine Test SCDO:0001207 Any measurement of protein present in urine. Suggest update to description in CMO. Suggest update to description (currently no description provided). CMO:0000770 Urinary Protein Measurement SCDO:0001208 The organs and passageways concerned with the production and excretion of urine, including the kidneys, ureters, urinary bladder, and urethra. http://purl.obolibrary.org/obo/BTO_0003092 BTO:0003092 deprecated Urinary System true SCDO:0001209 The amount of albumin in a specified volume of urine. Suggest that the CMO removes the second part of the definition and puts as comment, as we have done. Also suggest the change to this second part. Suggest update to description CMO:0000130 Urinary Albumin Concentration Urinary Albumin Level Urine Albumin Level Urine albumin levels which are above normal but not detectable with routine protein testing are referred to as low level albuminuria (the old term is microalbuminuria). Because albuminuria may be affected by non-pathological factors (exercise, menstruation contamination, biological variability, etc.), abnormal values should be confirmed within 1-2 months. Urine Albumin Concentration SCDO:0001210 The amount of albumin excreted into the urine within a specified period of time. Suggest that the CMO removes the second part of the definition and puts as comment, as we have done. Also suggest the change to this second part. http://purl.obolibrary.org/obo/CMO_0000757 Suggest update to description CMO:0000757 Urinary Albumin Excretion Rate If the level of albumin in the urine is above normal but not high enough to be detectable with routine protein testing it is referred to as low level albuminuria (the old term is microalbuminuria). Urine Albumin Excretion Rate SCDO:0001212 A comparison of urine microalbumin, that is, a level of albumin in the urine which is above normal but not detectable with routine protein testing, to the amount of creatinine in a specified volume of urine. Often expressed as albumin concentration divided by creatinine concentration times 1000 mg per gram. Suggest update to description as we have done. http://purl.obolibrary.org/obo/CMO_0000384 Suggest update to description CMO:0000384 ACR ALBCREAT Albumin To Creatinine Protein Ratio Measurement Albumin-Creatinine Ratio Albumin/Creatinine Ratio Microalbumin/Creatinine Ratio UACR Urinary Albumin-Creatinine Ratio Urine Albumin Level to Urine Creatinine Level Ratio Urine Microalbumin-Creatinine Ratio Urine Albumin-Creatinine Ratio SCDO:0001213 The concentration of creatinine in a urine specimen. Request inclusion below "urine creatinine measurement" in the CMO. None SCDO (Jade Hotchkiss) Urinary Creatinine Concentration Urine Creatinine Amount Urine Creatinine Concentration Measurement Datum Urine Creatinine Level Urine Creatinine Concentration SCDO:0001215 A method in which sulfosalicylic acid (that is, the SSA reagent) is added to a small and equal volume of clear urine. The acidification causes precipitation of protein in the sample (seen as increasing turbidity), which can be subjectively quantitated visually or more precisely quantitated using photometry. http://purl.obolibrary.org/obo/MMO_0000504 Sufficient SCDO:0001215 MMO:0000504 SSA Protein Precipitation Test Urine SSA Turbidimetry Urine Sulfosalicylic Acid Turbidimetry Urine Turbidimetry with Sulfosalicylic Acid Urine Protein Sulfosalicylic Acid Precipitation Test SCDO:0001218 The medical specialty concerned with the study, diagnosis, and treatment of diseases of the genitourinary tract. http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C17243 NCIT:C17243 obsolete Urology true SCDO:0001223 Works consisting of research using processes by which the reliability and relevance of a procedure for a specific purpose are established. http://purl.bioontology.org/ontology/MESH/D023361 Sufficient SCDO:0001223 MESH:D023361 Validation Studies SCDO:0001224 Smoking vapors produced from electronic nicotene delivery systems. http://purl.bioontology.org/ontology/MESH/D000072137 Sufficient SCDO:0001224 MESH:D000072137 Electronic Cigarrete Use Vaping SCDO:0001228 A measure of vascular endothelial cell response to stimulation, for example, by vasoactive substances released by or those that interact with the vascular endothelium. Request inclusion into relevant ontology http://circ.ahajournals.org/content/108/17/2054 None Assessment of Endothelial Cell Function Endothelium Dysfunction Test Vascular Endothelial Function Test Endothelial Function Test SCDO:0001229 Pain resulting from tissue ischemia as a result of blockage of blood vessels, occurring in a variety of vascular beds, but most commonly in the bone or bone marrow and requiring analgesic medication. Request inclusion into relevant ontology Evidence-Based Management of Sickle Cell Disease: Expert Panel Report (EPR), 2014 Few but definitions not specific enough SCDO Acute Pain Crisis Sickle Crisis VOC Vaso-Occlusive Crisis Vaso-Occlusive Episodes Vaso-Occlusive Crisis SCDO:0001230 Extraction of blood from a vein using a needle. In human, the basilic, cephalic and median cubital veins are most commonly used as well as the femoral vein. http://purl.obolibrary.org/obo/MMO_0000090 Sufficient SCDO:0001230 MMO:0000090 Venipuncture SCDO:0001232 A parent or caregiver questionnaire administered as part of a structured interview that measures day-to-day performance on communication, daily living, socialization, and motor skills. Standard scores can be derived for communication, daily living, socialization, and motor skills subtests or combined to create an Adaptive Behavior Composite (ABC). Suggest update to label in PhenX as we have done. http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820601 PhenX protocol: Adaptive Behavior/Adaptive Function #820601 Proxy This measure can be used to identify individuals with developmental disabilities or delays, perform diagnostic evaluations, monitor progress, and develop programs. All ages from birth through age 90 Suggest update to label phenX:820601 VABS Vineland Adaptive Behavior Scales Vineland-II Vineland Adaptive Behavior Scales, Second Edition (Vineland-II) SCDO:0001234 Minute infectious agents whose genomes are composed of DNA or RNA, but not both. They are characterized by a lack of independent metabolism and the inability to replicate outside living host cells. Add sub-classes: Hepatitis C Virus (term in NCIT) Hepatitis B Virus (term not found in other ontologies) http://purl.bioontology.org/ontology/MESH/D014780 Sufficient SCDO:0001234 MESH:D014780 Viruses Virus SCDO:0001237 Removal of the whole or part of the vitreous body in treating endophthalmitis, diabetic retinopathy, retinal detachment, intraocular foreign bodies, and some types of glaucoma. http://purl.bioontology.org/ontology/MESH/D014821 Sufficient SCDO:0001237 MESH:D014821 Vitrectomies Vitrectomy SCDO:0001240 Identification of proteins or peptides that have been electrophoretically separated by blot transferring from the electrophoresis gel to strips of nitrocellulose paper, followed by labeling with antibody probes. Can this term also be below "Immunological Assay"? Sufficient SCDO:0001240 MESH:D015153 Western Immunoblot Western Blot SCDO:0001241 An acute onset of wheezing in a person with SCD and co-morbid asthma. Glassberg, Jeffrey A., Robert Strunk, and Michael R. DeBaun. “Wheezing in Children with Sickle Cell Disease.” Current opinion in pediatrics 26.1 (2014): 9–18. PMC. Web. 2 Aug. 2017. Paediatr Respir Rev. 2014 Mar;15(1):13-6. doi: 10.1016/j.prrv.2013.10.005. Epub 2013 Oct 31. Synergistic inflammatory response due to both SCD and asthma. Increased severity of episodes. None SCDO Glassberg, Jeffrey A., Robert Strunk, and Michael R. DeBaun. “Wheezing in Children with Sickle Cell Disease.” Current opinion in pediatrics 26.1 (2014): 9–18. PMC. Web. 2 Aug. 2017. Paediatr Respir Rev. 2014 Mar;15(1):13-6. doi: 10.1016/j.prrv.2013.10.005. Epub 2013 Oct 31. Asthma Attack Wheezing Episode with Co-Morbid Asthma SCDO:0001246 An act of employing sorcery (the use of power gained from the assistance or control of spirits), especially with malevolent intent, and the exercise of supernatural powers and alleged intercourse with the devil or a familiar. (From Webster, 3rd Ed). http://purl.bioontology.org/ontology/MESH/D018599 Sufficient SCDO:0001246 MESH:D018599 Sorceries Sorcery Witchcraft SCDO:0001247 The WHOQOL is a quality of life assessment developed by the WHOQOL Group with fifteen international field centres, simultaneously, in an attempt to develop a quality of life assessment that would be applicable cross-culturally. Request inclusion into NCIT below "Research or Clinical Assessment Tool". Still must add these annotation properties: -- validated for age ranges -- has cross-cultural adaptation -- freely available -- has translations Self Healthy people; Clinic patients Demonstrated validity with SCD populations; at least two publications using the measure None WHOQOL Group (1993). Measuring quality of life: The development of the World Health Organisation quality of life instrument (WHOQOL). Geneva: WHO. WHOQOL World Health Organisation Quality of Life Instrument World Health Organisation Quality of Life Instrument (WHOQOL) SCDO:0001249 The visual output that an X-ray machine produces. Request inclusion into relevant ontology. Not relevant to context of sickle cell SCDO (Jade Hotchkiss) X-Ray Image SCDO:0001250 The visual output that an X-ray machine produces when imaging the chest. Request inclusion into relevant ontology. Negligable SCDO (Jade Hotchkiss) Chest X-Ray Image X-Ray Image of Chest SCDO:0001252 Medical treatment involving the use of controlled amounts of X-Rays. http://purl.bioontology.org/ontology/MESH/D014964 Sufficient SCDO:0001252 MESH:D014964 Roentgenotherapy X Ray Therapy X-ray Beam Therapy Xray Therapy X-Ray Therapy SCDO:0001253 Penetrating, high-energy electromagnetic radiation emitted when the inner orbital electrons of an atom are excited and release radiant energy. X-ray wavelengths range from 1 pm to 10 nm. Hard X-rays are the higher energy, shorter wavelength X-rays. Soft x-rays or Grenz rays are less energetic and longer in wavelength. The short wavelength end of the X-ray spectrum overlaps the gamma rays wavelength range. The distinction between gamma rays and X-rays is based on their radiation source. This should probably be removed. http://purl.bioontology.org/ontology/MESH/D014965 Sufficient SCDO:0001253 MESH:D014965 X-Radiation X-Ray Electromagnetic Radiation X-Rays SCDO:0001267 The EQ-5D is a widely-used generic instrument for describing health-related quality of life states in five dimensions scored from 1 to 3 or 1 to 5, and a visual analogue scale to record self-rated health state from 0 to100. These provide a simple descriptive profile and a single index value for health status. The EQ-5D can also be used to calculate health utilities and determine the quality-adjusted life years associated with a health state. There is also a youth version (EQ-5D-Y). The EuroQol Group. EuroQol-a new facility for the measurement of health-related quality of life. Health Policy. 1990; 16(3):199-208. Multiple countries and cultural groups Self Healthy People; Clinic Patients Widely used around the world, also used in SCD Adults and Youth (8 to 18 years) Few but definitions not specific enough Anie KA, Grocott H, White L, Dzingina M, Rogers G, Cho G (2012). Patient self-assessment of hospital pain, mood and health-related quality of life in adults with sickle cell disease. BMJ Open, 2, e001274. doi:10.1136/bmjopen-2012-001274. Howard, J, Malfroy, M, Llewelyn, C et al. The Transfusion Alternatives Preoperatively in Sickle Cell Disease (TAPS) study: a randomised, controlled, multicentre clinical trial. Lancet. 2013; 381(9870):930–938. The EuroQol Group. EuroQol-a new facility for the measurement of health-related quality of life. Health Policy. 1990; 16(3):199-208. EQ-5D EuroQol Five Dimension Self-Report Questionnaire EuroQol Five Dimensions Questionnaire EuroQol Five-Dimensional Questionnaire European Quality of Life Five Dimension Five Level Scale Questionnaire EuroQol Five Dimensions Questionnaire (EQ-5D) SCDO:0001268 The FACIT-Sp is a 12-item measure that asks participants to indicate how true various statements are about them on a Likert scale of 0 ("not at all") to 4 ("very much"). Responses on the FACIT-Sp are summed to create a total score, ranging from 0 to 48, with higher scores representing higher levels of spirituality. Request inclusion into NCIT below "Research or Clinical Assessment Tool". Peterman AH, Fitchett G, Brady MJ, et al. Measuring spiritual well-being in people with cancer: the functional assessment of chronic illness therapy—Spiritual Well-being Scale (FACIT- Sp). Ann Behav Med. 2002;24:49–58. Self; Proxy (Parent report) Children with SCD and their parents Demonstrated validity in SCD studies. Children and adults None Peterman AH, Fitchett G, Brady MJ, et al. Measuring spiritual well-being in people with cancer: the functional assessment of chronic illness therapy—Spiritual Well-being Scale (FACIT- Sp). Ann Behav Med. 2002;24:49–58. FACIT-Sp Scale Functional Assessment of Chronic Illness Therapy-Spirituality Scale Functional Assessment of Chronic Illness Therapy-Spirituality (FACIT-Sp) Scale SCDO:0001284 The application of modern theories of learning and conditioning in the treatment of behavior disorders. http://purl.bioontology.org/ontology/MESH/D001521 Sufficient SCDO:0001284 MESH:D001521 Behavior Modification Behavior Modifications Behavior Therapies Behavior Therapy Conditioning Therapies Conditioning Therapy Behaviour Therapy SCDO:0001288 A primary headache disorder that is characterized by severe, strictly unilateral pain which is orbital, supraorbital, temporal or in any combination of these sites, lasting 15-180 min. occurring 1 to 8 times a day. The attacks are associated with one or more of the following, all of which are ipsilateral: conjunctival injection, lacrimation, nasal congestion, rhinorrhea, facial sweating, eyelid edema, and miosis. http://purl.bioontology.org/ontology/MESH/D003027 Sufficient SCDO:0001288 MESH:D003027 Acute Severe Headache Cluster Headaches Migraine, Neuralgic Cluster Headache SCDO:0001292 Broad term used to describe several different acute conditions occurring with sickle cell disease, including aplastic crisis, hemolytic crisis, and vasoocclusive crisis. Sufficient SCDO:0001292 http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.00 ICD10CM:D57.00 D57.00 Hb-SS disease with (painful) crisis NOS Hb-SS disease with crisis, unspecified Hb-SS disease with vasoocclusive pain NOS Hemoglobin S sickling disorder with crisis Sickle cell anemia, crisis D57.00 Hb-SS disease with crisis, unspecified SCDO:0001295 An instrument used in the detection and diagnosis of heart abnormalities that measures electrical potentials on the body surface and generates a record of the electrical currents associated with heart muscle activity. Request inclusion into relevant ontology http://en.wiktionary.org/wiki/electrocardiograph Few but definitions not freely available Cardiograph Electrocardiographic Instrument Electrocardiograph SCDO:0001296 The transfer of erythrocytes from a donor to a recipient or reinfusion to the donor. http://purl.bioontology.org/ontology/MESH/D017707 Sufficient SCDO:0001296 MESH:D017707 Erythrocyte Transfusions Red Blood Cell Transfusion Red Blood Cell Transfusions Transfusion, Erythrocyte Transfusions, Erythrocyte Erythrocyte Transfusion SCDO:0001299 Works consisting of studies determining the effectiveness or utility of processes, personnel, and equipment. http://purl.bioontology.org/ontology/MESH/D023362 Sufficient SCDO:0001299 MESH:D023362 Evaluation Studies SCDO:0001303 Repetitive withdrawal of small amounts of blood and replacement with donor blood until a large proportion of the blood volume has been exchanged. Used in treatment of fetal erythroblastosis, hepatic coma, sickle cell anemia, disseminated intravascular coagulation, septicemia, burns, thrombotic thrombopenic purpura, and fulminant malaria. Sufficient SCDO:0001303 MESH:D005078 Exchange Blood Transfusion Exchange Transfusion, Whole Blood SCDO:0001304 An interviewer-administered test to measure a respondent's system of high-level cognitive functions such as abstract thinking, rule acquisition, cognitive flexibility, and goal-oriented behavior. Sufficient SCDO:0001304 phenX:131100 Executive Function Measure SCDO:0001312 The organ of vision that consists of the eyeball and the optic nerve. http://medical-dictionary.thefreedictionary.com/eye Oculus deprecated Eye true SCDO:0001316 Facial paralysis is loss of facial movement because of nerve damage. Is this not the same thing as "Facial Nerve Palsy"? DOID:13934 obsolete Facial Paralysis true SCDO:0001319 Inability to function due to tiredness related to sickle cell disease. Use the literature cited here to link to other phenotypes. Not relevant to context of sickle cell Fatigability Fatigable Lassitude Tiredness Fatigue SCDO:0001320 Studies to determine the advantages or disadvantages, practicability, or capability of accomplishing a projected plan, study, or project. http://purl.bioontology.org/ontology/MESH/D005240 Sufficient SCDO:0001320 MESH:D005240 Feasibility Studies SCDO:0001321 A potent narcotic analgesic, abuse of which leads to habituation or addiction. It is primarily a mu-opioid agonist. Fentanyl is also used as an adjunct to general anesthetics, and as an anesthetic for induction and maintenance. Were these specific synonyms selected form the long list in the description source because of specific relevance to SCD? Sufficient SCDO:0001321 MESH:D005283 Duragesic Durogesic N-phenyl-N-[1-(2-phenylethyl)piperidin-4-yl]propanamide Phentanyl Fentanyl SCDO:0001322 A bioassay to measure the serum concentration of ferritin (i.e., iron). Suggest update to label in PhenX (from "Serum or Plasma Ferritin") Suggest update to label phenX:811301 Ferritin Blood Test Ferritin Measurement Plasma Ferritin Assay Plasma Ferritin Test Serum Ferritin Assay Serum Ferritin Test SCDO:0001323 The amount of ferritin found in a specified volume of serum. Suggest update to description and label of "ferritin measurement" in the EFO. Suggest update to description SCDO (Jade Hotchkiss) Blood Serum Ferritin Concentration Blood Serum Ferritin Concentration Measurement Datum Serum Ferritin Level SCDO:0001325 An instrument which is used to count and sort microscopic particles suspended in a buffer. This instrument consists of a flow cell, at least one lamp or laser, a variable number of emission detectors or photomultipliers, a system that converts analog signals to digital, and a computer to run the system and collect and analyze the data output. Not sure whether this can be classified as a "Medical Device". http://purl.bioontology.org/ontology/npo#NPO_1769 Sufficient SCDO:0001325 NPO:1769 Flow Cytometer SCDO:0001326 Flow cytometry uses the principles of light scattering and fluorescence from fluorochrome molecules to generate specific multi-parameter data from particles and cells in the size range of 0.5um to 40um diameter. Sufficient SCDO:0001326 BAO:0000005 Flow Cytometry SCDO:0001327 Visualization of a vascular system after intravenous injection of a fluorescein solution. The images may be photographed or televised. It is used especially in studying the retinal and uveal vasculature. http://purl.bioontology.org/ontology/MESH/D005451 Sufficient SCDO:0001327 MESH:D005451 Fluorescence Angiography Fluorescein Angiography SCDO:0001328 A rare neurologic movement disorder characterized by sustained muscle contractions of a single body region, usually producing twisting and repetitive movements or abnormal postures or positions. Sufficient SCDO:0001328 ORPHA:1866 Focal Dystonia SCDO:0001329 A member of the vitamin B family that stimulates the hematopoietic system. It is present in the liver and kidney and is found in mushrooms, spinach, yeast, green leaves, and grasses (poaceae). Folic acid is used in the treatment and prevention of folate deficiencies and megaloblastic anemia. Sufficient SCDO:0001329 MESH:D005492 Folacin Folate Folvite L-Glutamic acid, N-(4-(((2-amino-1,4-dihydro-4-oxo-6-pteridinyl)methyl)amino)benzoyl)- Pteroylglutamic Acid Vitamin B9 Vitamin M Folic Acid SCDO:0001330 Studies in which individuals or populations are followed to assess the outcome of exposures, procedures, or effects of a characteristic, e.g., occurrence of disease. http://purl.bioontology.org/ontology/MESH/D005500 Sufficient SCDO:0001330 MESH:D005500 Follow Up Studies Follow-Up Study Followup Studies Follow-Up Studies SCDO:0001334 An observable characteristic of disease that is persistent and long standing. Request inclusion into relevant ontology http://purl.obolibrary.org/obo/NCIT_C14141 http://semanticscience.org/resource/SIO_010056 None SCDO (Clair Ingram) NCIT:C14141 SIO:010056 Chronic Phenotype SCDO:0001336 Terms deprecated in the "Phenotype" class. from phenotype SCDO:0001339 A questionnaire to measure the health status of individuals who had a stroke. Sufficient SCDO:0001339 phenX:820700 Functionality After Stroke Diagnostic Instrument Functionality After Stroke Measure SCDO:0001340 'The system concerned with the function and disorders of the gastrointestinal tract, including stomach, intestines, and associated organs including liver, pancreas and gall bladder. [Curator team: []]' http://medical-dictionary.thefreedictionary.com/gastroenterology gastrointestinal tract deprecated Gastrointestinal System true SCDO:0001342 Combined effects of genotypes and environmental factors together to affect phenotypic characteristics. http://purl.bioontology.org/ontology/MESH/D059647 Sufficient SCDO:0001342 MESH:D059647 Gene-Environment Interaction SCDO:0001369 Deviation(s) in the nucleotide sequence of the genetic material of an individual from that typical of the group to which the individual belongs, or deviation(s) in the nucleotide sequence of the genetic material of offspring from that of its parents. Suggest update to description in NCIT http://purl.obolibrary.org/obo/NCIT_C17248 Suggest update to description NCIT:C17248 Genetic Variation SCDO:0001373 'To be defined by an expert [Curator team: []]' made a synonym of HBB, GLU6LYS deprecated beta C mutation true SCDO:0001374 obsolete heterozygous beta c mutation true SCDO:0001375 obsolete homozygous beta c mutation true SCDO:0001376 'To be defined by an expert [Curator team: []]' Made a synonym of "HBB, GLU26LYS" deprecated beta E mutation true SCDO:0001377 'To be defined by an expert [Curator team: []]' Made a synonym of HBB, GLU6VAL deprecated beta S mutation true SCDO:0001378 This gene provides instructions for making a protein called alpha-globin, which is involved in oxygen transport. This protein is also produced from a nearly identical gene called HBA2. Suggest update to description in NCIT. http://www.ontobee.org/ontology/NCIT?iri=http://purl.obolibrary.org/obo/NCIT_C75429 Suggest update to description NCIT:C75429 HBA1 Gene Hemoglobin Subunit Alpha 1 Gene Hemoglobin, Alpha 1 Gene HBA1 SCDO:0001379 This gene provides instructions for making a protein called alpha-globin, which is involved in oxygen transport. This protein is also produced from a nearly identical gene called HBA1. Suggest update to description in NCIT. http://purl.obolibrary.org/obo/NCIT_C75432 Suggest update to description HBA2 Gene Hemoglobin Subunit Alpha 2 Gene Hemoglobin, Alpha 2 Gene HBA2 SCDO:0001382 Gamma Globin is a type of polypeptide chain that when in combination with alpha globin chains forms fetal hemoglobin. Beta-Hemoglobin subunits gamma-1 (147 aa, ~16 kDa) and gamma-2 (147 aa, ~16 kDa) are encoded by the human HBG1 and HBG2 gene respectively, in the beta-globin gene cluster. These proteins play a role in the transport of oxygen to tissues of the fetal body. Request inclusion into relevant ontology. https://www.genecards.org/cgi-bin/carddisp.pl?gene=HBG1 None Gamma-Globin Haemoglobin Gamma Chain Haemoglobin Subunit Gamma Hemoglobin Gamma Chain Hemoglobin Subunit Gamma SCDO:0001384 A reduction in the ratio of production of alpha globin to that of gamma globin. Request inclusion into the HPO below "Imbalanced Hemoglobin Synthesis". None SCDO (Nicole Vasilevsky) Increased Gamma/Alpha Synthesis Ratio Reduced Alpha/Gamma Synthesis Ratio SCDO:0001385 The state, in utero or shortly after birth, in which all four alpha globin genes are deleted or inactivated resulting in absent alpha globin synthesis. If gamma globin synthesis persists, then the resulting phenotype is hemoglobin Barts (four gamma chains) and hemoglobin Bart hydrops fetalis. Request inclusion into HPO below "Reduced Alpha/Gamma Synthesis Ratio" (also requested for inclusion). Marengo-Rowe, A.J., 2007, January. The thalassemias and related disorders. In Baylor university medical center proceedings (Vol. 20, No. 1, pp. 27-31). Taylor & Francis. None SCDO (Clair Ingram) Absence of Alpha Globin Synthesis with Gamma Globin Synthesis SCDO:0001386 A deletion in or of the HBA1 or HBA2 gene that can result in some form of alpha thalassemia. Request inclusion into relevant ontology Still need to add one sub-class: the complete deletion of the HBA1 and HBA2 genes on one chromosome 16, combined with a defect (deletional or nondeletional) in either the HBA1 or HBA2 gene on the other chromosome 16, leaving one functioning gene present (https://www.snpedia.com/index.php/Alpha_Thalassemia) None SCDO (Clair Ingram) Alpha-Globin Cluster Deletion Alpha-Globin Gene Cluster Deletion HBA Locus Deletion Alpha-Globin Locus Deletion SCDO:0001387 Deletion of all four alpha-globin genes resulting in the most severe form of alpha thalassemia, Hemoglobin Barts Hydrops Fetalis. Request inclusion into relevant ontology None SCDO (Clair Ingram) Homozygous Deletion of HBA1 and HBA2 SCDO:0001388 Mutagenesis where the mutation is caused by the introduction of foreign DNA sequences into a gene or extragenic sequence. This may occur spontaneously in vivo or be experimentally induced in vivo or in vitro. Proviral DNA insertions into or adjacent to a cellular proto-oncogene can interrupt genetic translation of the coding sequences or interfere with recognition of regulatory elements and cause unregulated expression of the proto-oncogene resulting in tumor formation. http://purl.bioontology.org/ontology/MESH/D016254 Sufficient SCDO:0001388 MESH:D016254 Gene Insertion Insertion Mutation Insertion SCDO:0001436 The administration of oxygen to an individual. It is of paramount importance in the peri-operative care of SCD patients as hypoxaemia predisposes to sickling. Few but definitions not specific enough Supplemental Oxygen Therapy Oxygen Therapy SCDO:0001511 Renal medullary carcinoma is a rare, aggressive subtype of renal cell carcinoma characterized by a large, white or tan, firm, infiltrative tumor with microabscess-like foci centered in the renal medulla, typically presenting with hematuria, abdominal/flank pain, weight loss and fever. It is associated with sickle cell trait and disease and metastasis to the bones and lungs is common at time of diagnosis. http://www.orpha.net/ORDO/Orphanet_319319 Sufficient SCDO:0001511 Shetty A, Matrana MR. Renal medullary carcinoma: a case report and brief review of the literature. Ochsner J. 2014;14(2):270-5. ORPHA:319319 Kidney Medullary Carcinoma RMC Renal Medullary Cancer Renal Medullary Carcinoma SCDO:0001551 A part of anthropological linguistics concerned with the interrelation between a language and the cultural behavior of those who speak it. Sufficient SCDO:0001551 APAONTO:Ethnolinguistics Ethnolinguistics SCDO:0001604 That period when the patient with sickle cell anaemia is free of infection, pain, or other disease processes. Request inclusion into relevant ontology. Juwah, A. I., Nlemadim, E. U., & Kaine, W. (2004). Types of anaemic crises in paediatric patients with sickle cell anaemia seen in Enugu, Nigeria. Archives of disease in childhood, 89(6), 572-576. Not relevant to context of sickle cell SCD Steady State Steady State SCDO:0001611 A reduction in the level of performance of the kidneys in areas of function comprising the concentration of urine, removal of wastes, the maintenance of electrolyte balance, homeostasis of blood pressure, and calcium metabolism. deprecated-Renal Insufficiency true SCDO:0001624 Not anemic, i.e. no reduction in erythrocytes volume and/or hemoglobin concentration. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) Nonanemic Non-Anemic SCDO:0001626 An amino acid-specifying codon that has been converted to a stop codon by mutation. Its occurance is abnormal causing premature termination of protein translation and results in production of truncated and non-functional proteins. A nonsense mutation is one that converts an amino acid-specific codon to a stop codon. http://purl.bioontology.org/ontology/MESH/D018389 Sufficient SCDO:0001626 MESH:D018389 Nonsense Codon SCDO:0001715 Chronic pain caused by damage to nerve fibers. It is usually associated with tissue injury. This pain is usually described as burning, numb, tingling, lancinating, shooting, or paroxysmal in nature and is associated with a sensation of pins and needles. Its severity is also enhanced by exposure to either cold or heat. This term already exists in the ontology as 'Chronic Neuropathic Pain' (SCDO:0000228), however when searching other ontologies, the term 'chronic' is included in the definition. I have therefore edited the definition to include the term 'chronic'. Please review as to whether we need to change the label that currently exists in SCDO. Is treated with: amitriptyline, duloxetine, gabapentin, or pregabalin. deprecated-Neuropathic Pain true SCDO:0001751 Deletion of both HBA2 genes, which results in an alpha-thal-2 (alpha-/alpha-) form of alpha thalassemia trait. With this deletion there is nearly normal production of red blood cells, but there may be a mild anemia. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) Trans Deletion of HBA2 Homozygous Deletion of HBA2 SCDO:0001765 A mutation in the beta-globin gene, HBB, that results in reduced beta globin synthesis. Request inclusion into relevant ontology None SCDO Beta-Minus Thalassemia Mutation SCDO:0001851 A rapid heartrate that exceeds the range of the normal resting heartrate for age, gender or patient population. Suggest update to description in HPO. The original description stated 'A rapid heartrate that exceeds the range of the normal resting heartrate for age', however I think it should be recommended that gender and patient population be included. http://purl.obolibrary.org/obo/HP_0001649 Suggest update to description HP:0001649 Fast Heart Rate Heart Racing Racing Heart Tachycardia SCDO:0001997 The process whereby a mutation in a hemoglobin molecule causes conformational changes in the hemoglobin molecule, which cause increased hydrophobicity of the molecule, which result in the formation of crystals consisting of the mutated hemoglobin molecules. This type of crystallisation is observed in hemoglobins with the HbC mutation. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) Crystallisation of Haemoglobin Crystallization of Haemoglobin Crystallization of Hemoglobin Haemoglobin Crystallisation Haemoglobin Crystallization Hemoglobin Crystallisation Hemoglobin Crystallization Crystallisation of Hemoglobin SCDO:0002039 A deficiency of the essential metal Zinc; an essential cofactor for many enzymes. Zinc deficiency is caused by a lack of zinc in the diet, loss of zinc after absorption, for example through loss through burns, inability to absorb Zinc, or increased loss through exercise. Sufficient SCDO:0002039 EFO:1000003 Zinc Deficiency SCDO:0002106 Insufficiency of arterial or venous blood supply to the spleen due to emboli, thrombi, vascular torsion, or pressure that produces a macroscopic area of necrosis. http://www.ebi.ac.uk/efo/EFO_1001190 Sufficient SCDO:0002106 EFO:1001190 Splenic Infarction SCDO:0002107 This represents the phenotypic feature of mutational effects on a given property of an organism biological system [Gaston K. Mazandu, []]. deprecated-Nature of Mutations true SCDO:0002125 The privacy of information and its protection against unauthorized disclosure. http://purl.bioontology.org/ontology/MESH/D003219 Sufficient SCDO:0002125 MESH:D003219 Privileged Communications Confidentiality SCDO:0002130 The pattern of gene expression at the level of genetic transcription in a specific organism or under specific circumstances in specific cells. http://purl.bioontology.org/ontology/MESH/D059467 Sufficient SCDO:0002130 MESH:D059467 Gene Expression Levels Gene Expression Profile Gene Expression Profiles Transcriptome SCDO:0002240 The presence and extensiveness of a disease in the body. It is objectively evaluated through diagnostic testing and physiological examination of the impaired biological organs or tissues, in cases in which disease severity can be distinguished from other realms of health, as in heart disease. Request inclusion into relevant ontology. This exists in the Influenza Ontology, but their definition is not ideal. Negligable Severity Disease Severity SCDO:0002243 Reimbursement of research participants for costs directly incurred during the research, such as travel costs and reasonable compensation for their inconvenience and time spent. Compensation can be monetary or non-monetary. Request inclusion into relevant ontology The label for this term has been changed to be more specific than the original "Compensation". International Ethical Guidelines for Health-related Research Involving Humans, Fourth Edition. Geneva, Council for International Organizations of Medical Sciences (CIOMS); 2016. Few but definitions not freely available SCDO (Jade Hotchkiss) Study Participant Compensation Research participants should be reasonably reimbursed for costs directly incurred during the research, such as travel costs, and compensated reasonably for their inconvenience and time spent. Compensation can be monetary or non-monetary. Compensation must not be so large as to induce potential participants to consent to participate in the research against their better judgment ("undue inducement"). A local research ethics committee must approve reimbursement and compensation for research participants. Research Participant Compensation SCDO:0002305 A mutation wholly or partly responsible for causing Hemoglobin D Disease. None SCDO (Jade Hotchkiss) Hemoglobin D Disease Causal Mutation SCDO:0002337 The abiding by applicable principles such as 1. compliance by research institutions; 2. obtaining and documenting informed consent; 3. Research Ethics Committee membership function, operations, review of research, and record keeping; 4. additional protection for certain vulnerable research subjects - pregnant women, prisoners, and children Request inclusion into relevant ontology National Commission for the Protection of Human Subjects of Biomedical and Behavioral Research. The Belmont Report: Ethical Principles and Guidelines for the Protection of Human Subjects of Research. [Bethesda, Md.] Research ethics committees: Basic concepts for capacity building. International Ethical Guidelines for Health-related Research Involving Humans, Fourth Edition. Geneva. Council for International Organizations of Medical Sciences (CIOMS); 2016. The Commission, 1978. World Health Organization. Geneva: WHO Document Production Services; 2009. None SCDO Ethical Conduct SCDO:0002475 A mutation in the beta-globin gene, HBB, that results in absent beta globin synthesis. Request inclusion into relevant ontology None SCDO Beta Null Mutation Beta-Zero Thalassemia Mutation SCDO:0002674 An abnormality of the body's metabolism or homeostasis. Suggest update to description in HPO. Currenlty the HPO does not have a description. Suggest update to description HP:0001939 Homeostasis Abnormality Metabolism Abnormality Abnormality of Metabolism/Homeostasis SCDO:0002798 Naturally occurring genetic variations associated with drug response. While these variants are not markers for genetic predisposition to disease, they influence pharmacokinetics and pharmacodynamics and often occur on genes encoding drug metabolism enzymes and transporters (e.g., angiotensin converting enzyme; cytochrome P-450 CYP2D6). Sufficient SCDO:0002798 MESH:D000071184 Pharmacogenomic Variants SCDO:0002814 'The hemoglobin molecule that transports oxygen in the blood is made up of a number of components. Human hemoglobin is a tetramer: in adults it is made up of two alpha globins and two beta globins; in the fetus, of two alpha and two g globins; and in the embryo, two e and two z globins. The sequences of these five globin types are similar and the genes that code for them occur in clusters on the chromosomes. In humans, there are two main clusters of globin genes: the alpha globin cluster on chromosome 16 and the beta globin cluster on chromosome 11. [Curator team: []]' http://www2.nau.edu/~bio372-c/class/evolution/glbgnclst.htm deprecated Globin Gene true SCDO:0002829 A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a material) to be used for testing, analysis, inspection, investigation, demonstration, or trial use. Sufficient SCDO:0002829 SIO:001050 Sample SCDO:0002939 Deoxygenated malfunctioning or mutated hemoglobins which clump together and form a long polymer in a process called polymerisation. Request inclusion in the HPO, below "Abnormal Hemoglobin". Description still needs work. None SCDO (Khuthala Mnika) Hemoglobin Polymer Polymerised Haemoglobin Polymerized Hemoglobin Sickle Hemoglobin Polymer Sickling Hemoglobin Polymerised Hemoglobin SCDO:0003028 A person's ethnic status, whether conserved or mixed ethnicity. Request inclusion into relevant ontology None SCDO (curators) Tribe Ethnic Status SCDO:0003065 Genetic variation in the structure leading to the abnomality of protein structure in non-sickle cell disease hemoglobin. Curation completed by the SCDO curator team: Clair. obsolete Non-SCD Structural Variants true SCDO:0003572 Documents describing a medical treatment or research project, including proposed procedures, risks, and alternatives, that are to be signed by an individual, or the individual's proxy, to indicate his/her understanding of the document and a willingness to undergo the treatment or to participate in the research. http://purl.bioontology.org/ontology/MESH/D032962 Sufficient SCDO:0003572 MESH:D032962 Consent Forms Consent Form SCDO:0003675 A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population. Sufficient SCDO:0003675 MESH:D020641 Single Nucleotide Polymorphism SCDO:0003696 A procedure in which a sample of peripheral blood is viewed under a microscope to count different circulating blood cells (red blood cells, white blood cells, platelets, etc.) and see whether the cells look normal. Request inclusion into relevant ontology None Peripheral Blood Film Examination Peripheral Blood Smear Peripheral Blood Film SCDO:0003712 A legal representation or family member of the participant gives consent on behalf of the patient. Request inclusion into the Informed Consent Ontology. MESH has the term Third-party consent, but the description's not suitable. None SCDO (Victoria Nembaware) Third-Party Consent Proxy Consent SCDO:0003736 Dynamic consent is a personalised, communication interface to enable greater participant engagement in clinical and research activities.The interface facilitates two-way communication to stimulate a more engaged, informed and scientifically literate participant population where individuals can tailor and manage their own consent preferences. It has the potential to be applied more broadly to situations where there are multiple and varied uses of data requiring different kinds of consent over a period of time. Request inclusion into ICO below "Informed Consent". https://www.nature.com/articles/ejhg201471 None SCDO Dynamic Consent SCDO:0003742 Surgical procedure involving either partial or entire removal of the spleen. Sufficient SCDO:0003742 MESH:D013156 Splenectomies Splenectomy SCDO:0003807 Hemoglobin characterized by structural alterations within the molecule that confer an inherited health condition phenotype. The alteration can be either absence, addition or substitution of one or more amino acids in the globin part of the molecule at selected positions in the polypeptide chains. Suggest HPO to update their term description and to move terms related to hemoglobin concentration below "Abnormal Hemoglobin Concentration". Include as a sub-class "Hemoglobin S-Providence"? Suggest update to description Abnormal Hemoglobin Variant Abnormal Hemoglobins Abnormal Variant of Hemoglobin Abnormal Hemoglobin SCDO:0003894 The polymerase chain reaction (PCR) is the most common method to detect the deletional thalassaemias. Gap-PCR amplifies the deleted DNA sequence using the primers flanking the deleted region 10. Three primers are designed for each deletion to amplify the normal (undeleted) and deleted gene sequences. Request inclusion into relevant ontology. Kho SL, Chua KH, George E, Tan JA. A novel gap-PCR with high resolution melting analysis for the detection of α-thalassaemia Southeast Asian and Filipino β°-thalassaemia deletion. Sci Rep. 2015;5:13937. Published 2015 Sep 14. doi:10.1038/srep13937 None Gap PCR SCDO:0004061 The genetic constitution of the individual, comprising the alleles present at each genetic locus. Sufficient SCDO:0004061 MESH:D005838 Genotype SCDO:0004078 Characterized by an established ileus, with vomiting, a silent distended abdomen and distended bowel loops and fluid levels on abdominal x-ray. Some hepatic enlargement is common, and it is often associated with bilateral basal lung consolidation (chest syndrome). Request inclusion into relevant ontology Can be treated with analgesia, IV fluids, and antibiotics if patient is febrile. SCD Management guidelines - Tanzania None SCDO Mesenteric Syndrome Girdle Syndrome SCDO:0004139 The most common and normal adult human hemoglobin tetramer, comprising over 97% of the total red blood cell hemoglobin and consisting of two alpha chains and two beta chains. Request inclusion into NCIT below "Hemoglobin"/"Normal Hemoglobin". Suggest update to description in MESH. Few but definitions not specific enough MESH:D006441 Adult Haemoglobin Haemoglobin A Haemoglobin A1 Hb A HbA Hemoglobin A Hemoglobin A1 alpha2beta2 Adult Hemoglobin SCDO:0004187 May be caused by an acute VOC, malarial infection or oxidant drug exposure in individuals with concomitant glucose-6-phosphate dehydrogenase (G6PD) deficiency. Haemolytic crisis may be distinguished from aplastic crisis by the finding of a reticulocytosis as opposed to a reticulocytopenia. Request inclusion into relevant ontology SCD Management guidelines - South Africa Few but definitions not freely available SCDO Hemolytic Crisis SCDO:0004277 A term used to express willingness to participate in research by persons who are by definition too young to give informed consent but who are old enough to understand the proposed research in general, its expected risks and possible benefits, and the activities expected of them as subjects. The source term seems to be deprecated in the ICO. Suggest update to description ICO:0000143 Assent SCDO:0004444 The protein product of the fusion of the gene products of the HBD and HBB genes that causes the mutation which causes the Hemoglobin Lepore Trait. Request inclusion into relevant ontology None Crossover between delta and beta globin gene loci Delta Beta Globin Chain Fusion Product Delta Beta Globin Fusion Chain SCDO:0004576 Chronic splenic sequestration associated with enlarged spleen and cytopaenia with anaemia and reduction in white blood cells and platelets. The anaemia is usually chronic in nature and patients rarely present with signs of heart failure. Request inclusion into the HPO below "Hypersplenism". Management of Sickle Cell Disease - The United Republic of Tanzania (By Ministry of Health) None SCDO Chronic Hypersplenism SCDO:0004598 The sequential set of three nucleotides in transfer RNA that interacts with its complement in messenger RNA, the Codon, during translation in the ribosome. http://purl.bioontology.org/ontology/MESH/D000926 Sufficient SCDO:0004598 MESH:D000926 Anticodon SCDO:0004623 Also known as sense codon, a set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (terminator codon). Most codons are universal, but some organisms do not produce the transfer RNAs complementary to all codons. These codons are referred to as unassigned codons (nonsense codons). Add "Terminator Codon" as a parent of "Nonsense Codon" as in MESH? http://purl.bioontology.org/ontology/MESH/D003062 Sufficient SCDO:0004623 MESH:D003062 Codon SCDO:0004716 A codon that directs initiation of protein translation (Translation, Genetic) by stimulating the binding of initiator tRNA (RNA, TRANSFER, MET). In prokaryotes, the codons AUG or GUG can act as initiators while in eukaryotes, AUG is the only initiator codon. http://purl.bioontology.org/ontology/MESH/D018387 Sufficient SCDO:0004716 MESH:D018387 Codon, Initiation Codon, Initiator Initiation Codon Initiation Codons Initiator Codons Start Codon Start Codons Initiator Codon SCDO:0004829 Brief reversible episodes of focal, nonconvulsive ischemic dysfunction of the brain having a duration of less than 24 hours, and usually less than one hour, caused by transient thrombotic or embolic blood vessel occlusion or stenosis. Events may be classified by arterial distribution, temporal pattern, or etiology (e.g., embolic vs. thrombotic). http://www.ebi.ac.uk/efo/EFO_0003764 Sufficient SCDO:0004829 EFO:0003764 Mini Stroke TIA Transient Ischemic Attacks Transient Ischemic Attack SCDO:0004836 A chest pain that is caused when your heart muscle doesn't get enough oxygen-rich blood. Sufficient SCDO:0004836 OAE:0002122 Angina SCDO:0004847 A rarely recognized complication of vaso-occlusive crisis. It is characterized by a presentation of right upper quadrant pain in the liver. A smooth, tender, enlarged liver is noted on physical exam. The lab values show a decrease in the hemoglobin/hematocrit. An increase in reticulocyte count is also seen. Request inclusion into relevant ontology Norris, W. E. (2004). Acute hepatic sequestration in sickle cell disease. Journal of the National Medical Association, 96(9), 1235-1239. The Management of Sickle Cell Disease. 1984. (Revised June 2002). NIH publication 02-2117. Available at http:/www.nhlbi.nih.gov/health/prof/blood/sickle/sc. None SCDO Acute Hepatic Sequestration SCDO:0004860 'A penicillin in which the substituent at position 6 of the penam ring is a 2-amino-2-(4-hydroxyphenyl)acetamido group. [Curator team: []]' http://purl.obolibrary.org/obo/CHEBI_2676 CHEBI:2676 deprecated-Amoxicillin true SCDO:0004888 An acquired disorder caused by several hematological and immunological diseases and characterized by impairment of splenic function. Request inclusion into relevant ontology, perhaps below "Abnormality of the Spleen" in the HPO. Few but definitions not freely available SCDO Kirkineska L, Perifanis V, Vasiliadis T. Functional hyposplenism. Hippokratia. 2014;18(1):7–11. Vijay, V., Cavenagh, J.D. and Yate, P., 1998. The anaesthetist's role in acute sickle cell crisis. British journal of anaesthesia, 80(6), pp.820-828. FH Functional Hyposplenism SCDO:0004905 Deletion of a part of the beta-globin locus. Request inclusion into relevant ontology None SCDO Beta-Globin Cluster Deletion Beta-Globin Gene Cluster Deletion Hemaglobin Beta Gene Deletion Beta-Globin Locus Deletion SCDO:0005167 Long lasting form of anemia. Request inclusion into relevant ontology No online description for this term exists, would it be sufficient to say 'Long lasting form of anemia'? or is there a better definition specific for sickle cell anemia? Few but definitions not freely available SCDO Chronic Anemia SCDO:0005191 An increase in the rate of hemolysis, in conjunction with specific clinical complications of sickle cell disease. Request inclusion into Mammalian Phenotype ontology below "Hemolysis". Info also provided by the definition source: 'Hyperhemolysis should be typified by an acute reduction in hemoglobin level associated with higher than usual reticulocyte counts and perhaps an unaccountable and sudden increase in LDH.' Request inclusion into relevant ontology Disorders of Hemoglobin: Genetics, Pathophysiology, and Clinical Management. Martin H. Steinberg, Bernard G. Forget, Douglas R. Higgs, David J. Weatherall. Cambridge University Press, 17 Aug 2009 None SCDO Hyperhemolysis SCDO:0005243 A method for comparing two sets of chromosomal DNA by analyzing differences in the copy number and location of specific sequences. It is used to look for large sequence changes such as deletions, duplications, amplifications, or translocations. Sufficient SCDO:0005243 MESH:D055028 CGH Comparative Genome Hybridization Comparative Genomic Analysis Comparative Genomic Hybridizations Comparative Genomic Hybridisation SCDO:0005279 An abnormally high number of reticulocytes per unit volume of blood. The normal fraction of reticulocytes in the blood depends on the clinical situation but is usually 0.5% to 2.5% in adults and 2% to 6% in infants. Request inclusion into relevant ontology Symptom of splenic sequestration, or increased haemolysis. Negligable SCDO (Jade Hotchkiss) Reticulocyte Count High deprecated High Reticulocyte Count true SCDO:0005339 The physical characteristics of the globin polypeptides that form hemoglobins. Request inclusion into relevant ontology. https://www.ncbi.nlm.nih.gov/pubmed/20339107 None Globin Chain Phenotype Globin Phenotype SCDO:0005379 Work consisting of a structured file of information or a set of logically related data stored and retrieved using computer-based means. http://purl.bioontology.org/ontology/MESH/D019991 Sufficient SCDO:0005379 MESH:D019991 Data Base Database SCDO:0005446 The major component of hemoglobin in the fetus. This hemoglobin has two alpha and two gamma polypeptide subunits in comparison to normal adult hemoglobin, which has two alpha and two beta polypeptide subunits. Fetal hemoglobin concentrations can be elevated (usually above 0.5%) in children and adults affected by leukemia and several types of anemia. Request inclusion into NCIT below "Hemoglobin"/"Normal Hemoglobin", for completion sake. Sufficient SCDO:0005446 MESH:D005319 Fetal Haemoglobin Foetal Haemoglobin Haemoglobin F Hb F HbF Hemoglobin F Fetal Hemoglobin SCDO:0005464 A disorder of cardiac function caused by insufficient blood flow to the muscle tissue of the heart. The decreased blood flow may be due to narrowing of the coronary arteries (coronary artery disease), to obstruction by a thrombus (coronary thrombosis), or less commonly, to diffuse narrowing of arterioles and other small vessels within the heart. Severe interruption of the blood supply to the myocardial tissue may result in necrosis of cardiac muscle (myocardial infarction). http://www.ebi.ac.uk/efo/EFO_1001375 Sufficient SCDO:0005464 EFO:1001375 Myocardial Ischemia SCDO:0005580 Avascular necrosis of femoral head (ANFH) is a severely disabling disease characterised by progressive groin pain, a limping gait, leg length discrepancy, collapse of the subchondral bone, limitation of hip function and eventual degeneration of the hip joint requiring total hip arthroplasty. http://www.orpha.net/ORDO/Orphanet_86820 Orphanet:86820 ANFH deprecated-Avascular Necrosis of the Femoral Head true SCDO:0005593 The meaning ascribed to the base sequence with respect to how it is translated into amino acid sequence. The start, stop, and order of amino acids of a protein is specified by consecutive triplets of nucleotides called codons. http://purl.bioontology.org/ontology/MESH/D005815 Sufficient SCDO:0005593 MESH:D005815 Genetic Code SCDO:0005671 Deletion of the HBB and HBD genes that results in delta-beta thalassemia. Request inclusion into relevant ontology None SCDO HBB and HBD Deletion SCDO:0005722 A biological object that contains genetic information and that is involved in transmitting genetically encoded traits from one organism to another. Sufficient SCDO:0005722 MESH:D040342 Genetic Structures Genetic Structure SCDO:0005927 An ethical principle that obligates one to treat people fairly. Distributive justice refers to allocating benefits and harms fairly; procedural justice refers to using fair processes to make decisions that affect people; formal justice refers to treating similar cases in the same way. In human subjects research, the principle of justice implies that subjects should be selected equitably. Request inclusion into relevant ontology https://www.niehs.nih.gov/research/resources/bioethics/glossary/index.cfm#human-subjects-research Few but definitions not specific enough SCDO Justice SCDO:0006000 Elevated body temperature due to failed thermoregulation, or inflammation or immune responses. Merged the two descriptions from NCIT and HP Suggest update to description in NCIT and HP. Suggest update to description HP:0001945 NCIT:C3038 Pyrexia Pyrogenic Reaction Fever SCDO:0006036 A person who has not attained the age at which full civil rights are accorded. http://purl.bioontology.org/ontology/MESH/D033242 Sufficient SCDO:0006036 MESH:D033242 Minor SCDO:0006070 An ethnic group that includes persons with significant ethnic contributions from more than one group. http://purl.obolibrary.org/obo/ERO_0002032 Sufficient SCDO:0006070 ERO:0002032 Mixed Ethnicity SCDO:0006339 Critical and exhaustive investigation or experimentation, having for its aim the discovery of new facts and their correct interpretation, the revision of accepted conclusions, theories, or laws in the light of newly discovered facts, or the practical application of such new or revised conclusions, theories, or laws. http://purl.bioontology.org/ontology/MESH/D012106 Sufficient SCDO:0006339 MESH:D012106 Research SCDO:0006429 An uncommon complication of cholecystitis and refers to a situation where the gallbladder lumen is filled and distended by purulent material (pus). Request inclusion into relevant ontology https://radiopaedia.org/articles/gallbladder-empyema Few but definitions not freely available SCDO Gallbladder Empyema SCDO:0006461 Aplasia or hemolysis may be precipitated by another illness/infection in sickle cell disease patients. Acutely severe anemia is defined as Hb < 5g/dl or a recent acute drop in HB > 2g/dl below the individual's steady state value. If no steady state value is available, it can be detected by the presence of acutely symptomatic anemia (i.e. tachycardia, cardiac failure, shock). Request inclusion into relevant ontology. Please check with the working group as to how they feel about the label for this term. SCD Management guidelines - Tanzania None SCDO Acutely Severe Anemia SCDO:0006517 Research involving the collection, storage, or use of private data or biological samples from living individuals by means of interactions, interventions, surveys, or other research methods or procedures. https://www.niehs.nih.gov/research/resources/bioethics/glossary/index.cfm#human-subjects-research Not relevant to context of sickle cell Human Subject Research SCDO:0006589 The collecting of fetal blood samples typically via endoscopic ultrasound guided fine needle aspiration from the umbilical vein, followed by examination of the blood to detect fetal abnormalities. Suggest update to description in MESH. Suggest update to description MESH:D017218 Fetal Blood Sampling PUBS Percutaneous Umbilical Cord Blood Sampling Umbilical Vein Sampling Cordocentesis SCDO:0006613 A material transfer agreement (MTA) is a type of legally enforceable contract employed by research institutions and companies to set the terms under which their materials and associated data may be obtained and used by others. Request inclusion into relevant ontology Henderson J (2007) Counterpoint: MTAs are a practical necessity. Nat Biotechnol 25: 722–724. None MTA Material Transfer Agreement SCDO:0006706 A branch of applied ethics that studies the value implications of practices and developments in life sciences, medicine, and health care. http://purl.bioontology.org/ontology/MESH/D001675 Sufficient SCDO:0006706 MESH:D001675 Biomedical Ethics Health Care Ethics Bioethics SCDO:0006832 A condition due to a dietary deficiency of ascorbic acid (vitamin C), characterized by malaise, lethargy, and weakness. As the disease progresses, joints, muscles, and subcutaneous tissues may become the sites of hemorrhage. Ascorbic acid deficiency frequently develops into SCURVY in young children fed unsupplemented cow's milk exclusively during their first year. It develops also commonly in chronic alcoholism. (Cecil Textbook of Medicine, 19th ed, p1177) Sufficient SCDO:0006832 MESH:D001206 Ascorbic Acid Deficiencies Vitamin C Deficiencies Vitamin C Deficiency Ascorbic Acid Deficiency SCDO:0006833 A rare intracranial arteriopathy involving progressive stenosis of the cerebral vasculature located at the base of the brain causing transient ischemic attacks or strokes. http://www.orpha.net/ORDO/Orphanet_2573 Sufficient SCDO:0006833 ORPHA:2573 MMD Moyamoya Disease SCDO:0006835 Hemoglobin that presents no inherited health condition phenotype. Request inclusion into NCIT below "Hemoglobin". Few but definitions not freely available SCDO (Jade Hotchkiss) Hemoglobin Normal Hemoglobin Normal Variant Normal Hemoglobin SCDO:0006847 An acute form of acquired red cell aplasia. A significant change in blood picture is observed, characterised by a precipitous fall in the haemoglobin level (>20 g/l beyond steady state level) and reduced (<1%) or absent reticulocytes in the peripheral blood. The total white blood cell or platelet counts may or may not be affected. In addition, there is no significant increase in the unconjugated fraction of serum bilirubin.The most common cause is infection by parvovirus B19, a DNA virus that replicates inside immature red blood cells in the bone marrow, resulting in severe anaemia (hemoglobin levels well below steady state) and low reticulocyte count. It is rarely recurrent. Request inclusion into relevant ontology Juwah, A. I., Nlemadim, E. U., & Kaine, W. (2004). Types of anaemic crises in paediatric patients with sickle cell anaemia seen in Enugu, Nigeria. Archives of disease in childhood, 89(6), 572-576. SCD Management guidelines - Jamaica SCD Management guidelines - Nigeria SCD Management guidelines - South Africa Few but definitions not freely available SCDO Aplastic Crises Aplastic Crisis SCDO:0006860 Mutations in the HBG1 and/or HBG2 genes. Such mutations can lead to variably increased levels of fetal hemoglobin (Hb) (Hb F, alpha2gamma2) in the syndrome of hereditary persistence of fetal Hb (HPFH). Request inclusion into relevant ontology. Perhaps add sub-classes of specific mutations as in the dc:source. None SCDO (Jade Hotchkiss) HBG1 and/or HBG2 Mutations SCDO:0006905 Condition characterized by splenomegaly, some reduction in the number of circulating blood cells in the presence of a normal or hyperactive bone marrow, and the potential for reversal by splenectomy. http://www.ebi.ac.uk/efo/EFO_1000975 Sufficient SCDO:0006905 Al-Salem, A. H. (2011). Splenic Complications of Sickle Cell Anemia and the Role of Splenectomy. ISRN Hematology, 2011, 864257. http://doi.org/10.5402/2011/864257 EFO:1000975 Hypersplenia Hypersplenism SCDO:0006909 Significant change in blood picture characterised by a precipitous fall in the haemoglobin level associated with jaundice, marked reticulocytosis, and polychromasia on the blood smear, increased unconju- gated hyperbilirubinaemia, and increased urobilinogen content in urine above the steady state level for each individual patient. Request inclusion into relevant ontology Juwah, A. I., Nlemadim, E. U., & Kaine, W. (2004). Types of anaemic crises in paediatric patients with sickle cell anaemia seen in Enugu, Nigeria. Archives of disease in childhood, 89(6), 572-576. None SCDO Hyper-Hemolytic Crisis SCDO:0006911 An ethnic group that includes persons with ethnic contributions from only one ethnic group. Request inclusion into relevant ontology None SCDO (curators) Conserved Ethnicity SCDO:0006921 Hemoglobin with altered structural and biochemical properties. Request inclusion into NCIT below "Hemoglobin". https://www.ncbi.nlm.nih.gov/pubmed/23388674 None SCDO (Clair Ingram) Hemoglobin Variant SCDO:0007087 Voluntary authorization, by a patient or research subject, with full comprehension of the risks involved, for diagnostic or investigative procedures, and for medical and surgical treatment. Sufficient SCDO:0007087 MESH:D007258 Informed Consent SCDO:0007161 Significant change in blood picture characterised by a precipitous fall in the haemoglobin level of at least 20 g/l and accompanied by a rapidly enlarging spleen or liver (greater than 2 cm from the steady state level) and reticulocytosis above the steady state level for each individual patient. Signs of acute circulatory insufficiency such tachypnoea, tachycardia, and hypotension may or may not be present. It is the earliest life-threatening complication seen in patients with SCD besides pneumococcal infections. Request inclusion into relevant ontology Vijay, V., Cavenagh, J.D. and Yate, P., 1998. The anaesthetist's role in acute sickle cell crisis. British journal of anaesthesia, 80(6), pp.820-828. Few but definitions not freely available SCDO Acute Crisis Splenic Sequestration Acute Splenic Sequestration Crisis SCDO:0007192 A hemoglobinopathy caused by a reduced or imbalanced synthesis of a normal globin chain or by a defect in the switch between synthesis of different types of normal hemoglobin. None SCDO (Jade Hotchkiss) Abnormal Hemoglobin Synthesis Abnormal Synthesis Hemoglobinopathy Synthesis Hemoglobinopathy Quantitative Hemoglobinopathy SCDO:0007212 'Other molecules are complexes which do not contain protein or RNA, including lipids, carbohydrates, etc.' obsolete Other Molecules true SCDO:0007281 Insufficient production of steroid hormones (primarily cortisol) by the adrenal glands as a result of a primary defect in the glands themselves. Suggest update to description. Not sure if they changed their description or if we adapted it. Suggest update to description HP:0000846 Hypoadrenalism Adrenal Insufficiency SCDO:0007495 The probability that an event will occur. It encompasses a variety of measures of the probability of a generally unfavorable outcome. http://purl.bioontology.org/ontology/MESH/D012306 Sufficient SCDO:0007495 MESH:D012306 Risk SCDO:0007519 A process of inclusive participation that supports mutual respect of values, strategies, and actions for authentic partnership of people affiliated by geographic location, shared interest, or similar circumstances to address issues affecting community wellbeing. Request inclusion into relevant ontology Holzer et al 2014 Doi:10.1097/JIM.0000000000000097 Few but definitions not available Community Engagement SCDO:0007565 Distinct geographical area. This term was too general. Was replaced by "Geographic Area". deprecated Major Area true SCDO:0007597 Information or a description of consent (hypothetical or obtained) or any aspect involved in or captured in the consent process. Request inclusion into relevant ontology, perhaps the ICO. None SCDO (Jade Hotchkiss) Descriptor of Consent SCDO:0007618 In situ death of bone within the humeral head due to disruption of blood supply. Has synonym: Osteonecrosis of the humeral head http://www.wheelessonline.com/ortho/Humeral_Head_Osteonecrosis deprecated-Avascular necrosis of the humeral head true SCDO:0007623 The molecular characteristics of a cell of tissue including expressed coding and non-coding RNAs, proteins and their post-translational modifications, lipids, carbohydrates and small molecules that characterize the state in a cell or tissue and that result from the interaction of its genotype and the environment. http://www.bioassayontology.org/bao#BAO_0170001 Sufficient SCDO:0007623 BAO:0170001 Molecular Phenotype SCDO:0007624 HBB genetic variants that result in reduced or absent hemoglobin subunit beta production. Request inclusion into relevant ontology PMID: 20301599 None SCDO Beta Thalassemia Genotype SCDO:0007656 Hemolytic anemia, in which patients are compound or double heterozygous for both the sickle cell gene and a thalassemia gene. Suggest update to description in NCIT Suggest update to description NCIT:C61237 Sickle Cell-Thalassemia Sickle Cell Thalassemia SCDO:0007897 A document containing the determination of the Research Ethics Committee (REC) that the clinical study with human subject participation has been reviewed and may be conducted at a particular study site within the constraints set forth by the REC and other institutional and federal requirements. The regulations require that an REC conduct continuing review of research at intervals appropriate to the degree of risk, but not less than once a year. Request inclusion into relevant ontology None SCDO Ethics Approval SCDO:0007900 Hemoglobin produced in the blood islands in the embryonic yolk sac during the mesoblastic stage of gestation. There are four different embryonic hemoglobins, Hemoglobin Gower 1, Hemoglobin Gower 2, Hemoglobin Portland 1 and Hemoglobin Portland 2. Request inclusion into NCIT below "Hemoglobin"/"Normal Hemoglobin". Add sub-classes: Hemoglobin Gower 1 Hemoglobin Gower 2 Hemoglobin Portland 1 Hemoglobin Portland 2 R Al-Mufti, H Hambley, F Farzaneh, KH Nicolaides Haematologica Jan 2000, 85 (7) 690-693; None Hemoglobin Epsilon Embryonic Hemoglobin SCDO:0008037 A seizure that occurs in the context of a brain insult (systemic, toxic, or metabolic) and may not recur when the underlying cause has been removed or the acute phase has elapsed. It is often associated with infections, infarctions, and severe metabolic or sickle cell complications. Suggest update to description in HPO. SCD Management guidelines - Jamaica Suggest update to description HP:0011145 Provoked Seizures Situation-Related Seizures Acute Symptomatic Seizure SCDO:0008251 Deletion of both HBA1 genes, which results in an alpha-thal-2 (alpha-/alpha-) form of alpha thalassemia trait. With this deletion there is nearly normal production of red blood cells, but there may be a mild anemia. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) Trans Deletion of HBA1 Homozygous Deletion of HBA1 SCDO:0008262 A hemoglobinopathy caused by the presence of structurally abnormal hemoglobins. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) Qualitative Hemoglobinopathy Structural Hemoglobinopathy SCDO:0008595 Persistence of an inflammatory event in the articulation overtime. Request inclusion into relevant ontology None SCDO Chronic Arthritis SCDO:0008623 The obstruction of blood vessels by altered erythrocytes that can result in pain, anemia and tissue ischemia. Request inclusion into relevant ontology None SCDO Vaso-Occlusion SCDO:0008625 Characterized by pain and discomfort in the right upper quadrant (RUQ) of the abdomen caused by a number of possible aetiologies in sickle cell disease. Causes of RUQ pain may be divided into pain originating from the liver or gall bladder versus other origins of abdominal pain in that region. Request inclusion into relevant ontology SCD Management guidelines - Jamaica Few but definitions not freely available RUQ Pain Right Upper Quadrant Pain Right Upper Quadrant Syndrome SCDO:0008688 A biobank is a collections of samples of biological substances (e.g. tissue, blood, DNA) which are linked to data about the samples and their donors. They have a dual nature as collections of samples and data and usually require investigators or institutions to agree to certain conditions as a condition for sharing samples or data with them. Suggest update to description in OMIABIS Suggest update to description OMIABIS:0000000 Biobank SCDO:0008713 The concurrence of sickle cell anemia and alpha-thalassemia. This condition is thought to result in less severe hemolytic anemia due to reduced concentration of hemoglobin S and its polymerization within red blood cells. Request inclusion into relevant ontology Few but definitions not freely available SCDO (Clair Ingram) Co-Inheritance of Alpha-Thalassemia and Sickle Cell Anemia Co-Inheritance of Sickle Cell Anemia and Alpha-Thalassemia Sickle Cell Anemia Associated with Coexistent Alpha Thalassemia Sickle Cell Anemia Associated with Alpha Thalassemia SCDO:0008778 A radiograph of dental structures made on x-ray film or stored as a digital image. The radiographs may be extraoral or intraoral. Three common types of intraoral dental images are periapical, interproximal, and occlusal radiographs. Request inclusion into relevant ontology "dental radiograph." Mosby's Medical Dictionary, 8th edition. 2009. Elsevier 7 Nov. 2018 https://medical-dictionary.thefreedictionary.com/dental+radiograph None Radiologic Examination, Teeth Dental Radiograph SCDO:0008888 The removal of excess iron from the body with special drugs. Request inclusion into MESH below "Chelation Therapy" None Iron Chelation Therapy SCDO:0008925 The capacity for self-governance, i.e. the ability to make reasonable decisions. Request inclusion into relevant ontology Few but definitions not freely available SCDO https://www.hhs.gov/ohrp/sites/default/files/the-belmont-report-508c_FINAL.pdf Autonomy SCDO:0008937 Blockage of blood flow in the central retinal artery. Results in sudden painless loss of vision and occurs in children and young adults. Thrombus formation in the retinal artery occurs spontaneously or in association with hyphema, Moyamoya and acute chest sydrome. There is no associated pain and it may be unilateral or bilateral. Suggest update to description in HPO SCD Management guidelines - Jamaica Suggest update to description HP:0025342 Central Retinal Artery Occlusion SCDO:0008990 Occurs where there is infarction of vertebral bone marrow, leading to collapse of the vertebrae with a typical 'fish mouth' appearance. It is often asymptomatic, but may cause acute and/or long term pain requiring analgesia and mechanical support such as a brace. Can be an acute or chronic bone problem in SCD. Suggest update to description in HPO (currently no description). Few but definitions not freely available SCDO HP:0002953 Compression Fracture Fractures of Vertebral Bodies Vertebral Body Compression Vertebral Compression Vertebral Compression Fractures Vertebral Compression or Collapse Vertebral Collapse SCDO:0009089 Principle dictating that harm should not come to individuals as a result of their participation in a research project. Request inclusion into relevant ontology Shamoo AE and Resnik DB, Responsible Conduct of Research, 3rd ed. (New York: Oxford University Press, 2015). None Non-Maleficience SCDO:0009117 A nutritional condition produced by a deficiency of folic acid in the diet. Alcohol interferes with its intermediate metabolism and absorption. Folic acid deficiency may develop in long-term anticonvulsant therapy or with use of oral contraceptives. This deficiency causes anemia, macrocytic anemia, and megaloblastic anemia. It is indistinguishable from vitamin B 12 deficiency in peripheral blood and bone marrow findings, but the neurologic lesions seen in B 12 deficiency do not occur. (Merck Manual, 16th ed) Sufficient SCDO:0009117 EFO:0001070 Deficiency of Folic Acid Deficiency of Folic Acid (Disorder) Folic Acid Deficiencies Folic Acid Deficiency Folate Deficiency SCDO:0009169 A hemoglobinopathy caused by compound heterozygous inheritance of one hemoglobin S allele and one hemoglobin allele that produces structurally abnormal hemoglobin. obsolete Sickle Plus Structural Variant true SCDO:0009279 Hemoglobin with decreased solubility in the red cell due to substitutions in the primary sequence of globin which alters the tertiary or quaternary structure of the molecule and results in a globin polypeptide/hemoglobin tetramer that is unstable and precipitates intracellularly, reducing the red blood cell lifespan. Request inclusion in the HPO, below "Abnormal Hemoglobin". Few but definitions not freely available SCDO (Jade Hotchkiss) Unstable Hemoglobin SCDO:0009350 An acute condition of intrasplenic pooling of large amounts of blood. Suggest update to description in the Radiology Lexicon, or use their description "Splenic sequestration occurs in sickle cell disease when sickled red blood cells become trapped in the spleen, causing it to enlarge." Suggest update to description SCDO Blood Trapped in the Spleen Can cause severely acute anemia. Splenic Sequestration SCDO:0009445 A complication of kidney diseases characterized by cell death involving kidney papilla in the kidney medulla. Damages to this area may hinder the kidney to concentrate urine resulting in polyuria. Sloughed off necrotic tissue may block kidney pelvis or ureter. Necrosis of multiple renal papillae can lead to kidney failure. http://www.ebi.ac.uk/efo/EFO_1001004 Sufficient SCDO:0009445 EFO:1001004 Kidney Papillary Necrosis Necrotising Renal Papillitis Necrotizing Renal Papillitis Papillary Necrosis Papillary Necrosis (Disorder) Renal Papillitis Necrotizing Renal Papillary Necrosis SCDO:0009488 'Any single chemical entity that is an electrically neutral entity consisting of more than one atom. Each atom carries a certain number of electrons that orbit around the nucleus.[Curator team: []]' http://purl.obolibrary.org/obo/CHEBI_25367 CHEBI:25367 obsolete Molecule true SCDO:0009532 Effort made to secure the well-being of persons, maximizing possible benefits and minimizing possible harms. https://www.hhs.gov/ohrp/sites/default/files/the-belmont-report-508c_FINAL.pdf Few but definitions not specific enough SCDO MESH:D026686 Beneficence SCDO:0009613 The physical characteristics and levels of proteins that characterize the state in a cell or tissue and that result from the interaction of its genotype and the environment. Request inclusion into BioAssay Ontology below "biochemical phenotype". Can all sub-classes of the "Gene Product" class not be included here? Can this class not be removed but its sub-classes kept? None SCDO (Jade Hotchkiss) Protein Phenotype SCDO:0009620 An abnormally low number of reticulocytes per unit volume of blood. Request inclusion into relevant ontology Symptom of aplastic crisis, possibly due to parvovirus B19 infection. Is there a certain value below which is considered a low reticulocyte count? Negligable SCDO (Jade Hotchkiss) deprecated Low Reticulocyte Count true SCDO:0009635 'The aplastic crisis is temporary cessation of red cell production. This usually affect sickle cell patients, because of the markedly shortened red cell survival time in patients with sickle cell disease, a precipitous drop in hemoglobin occurs in the absence of adequate reticulocytosis. [Curator team: []]' http://www.ihtc.org/medical-professionals/blood-disorders/sickle-cell-disease/aplastic-crisis-intervention/ deprecated Aplastic Crises true SCDO:0009664 Pain resulting from tissue ischemia as a result of blockage of mesenteric blood vessels. Request inclusion into relevant ontology Akingbola TS, Kolude B, Aneni EC, et al. ABDOMINAL PAIN IN ADULT SICKLE CELL DISEASE PATIENTS: A NIGERIAN EXPERIENCE. Annals of Ibadan Postgraduate Medicine. 2011;9(2):100-104. SCD Management guidelines - Tanzania Abdominal distension with generalised abdominal tenderness (no rebound tenderness) and reduced bowel sounds. Abdomen moves with respiration. Vomiting/diarrhoea are not common. None Abdominal Vaso-Occlusive Crisis SCDO:0009731 A mutation in the beta-globin gene, HBB, that causes decreased or absent beta-globin synthesis. Request inclusion into relevant ontology None SCDO Beta Thalassemia Mutation SCDO:0009786 A genetic mutation in the HBB gene that results in absent or decreased hemoglobin subunit beta or an abnormal hemoglobin other than Hb S. Too specific to SCD to be included in other ontologies. None SCDO Other HBB Variants SCDO:0009884 The proteins and their post-translational modifications, lipids, carbohydrates and small molecules that characterize the state in a cell or tissue and that result from the interaction of its genotype and the environment. Sufficient SCDO:0009884 BAO:0170003 Biochemical Phenotype SCDO:0010000 'Genotypes which are not specific to sickle cell trait.' obsolete Other Genotypes true SCDO:0300002 The moral obligations governing the conduct of research. Used for discussions of research ethics as a general topic. http://purl.bioontology.org/ontology/MESH/D032984 Sufficient SCDO:0300002 MESH:D032984 Research Ethics SCDO:0300003 Specific genre of publication. http://purl.bioontology.org/ontology/MESH/D052180 Sufficient SCDO:0300003 MESH:D052180 Publication Formats SCDO:0300004 Types and formulations of studies used in epidemiological and clinical research. Suggest update to description in MESH http://purl.bioontology.org/ontology/MESH/D016020 Suggest update to description MESH:D016020 Epidemiologic Study Characteristics SCDO:0300005 Elements, types, descriptions and formulations of a research study. Request inclusion into relevant ontology None SCDO (Gaston K. Mazandu) Research Characteristics SCDO:0300006 Revealing of information, by oral or written communication. http://purl.bioontology.org/ontology/MESH/D030881 Sufficient SCDO:0300006 MESH:D030881 Information Disclosure SCDO:0300007 Reporting to parents or guardians about care to be provided to a minor (minors). http://purl.bioontology.org/ontology/MESH/D035622 Sufficient SCDO:0300007 MESH:D035622 Parental Notification SCDO:0300008 A legal requirement that designated types of information acquired by professionals or institutions in the course of their work be reported to appropriate authorities. http://purl.bioontology.org/ontology/MESH/D019221 Sufficient SCDO:0300008 MESH:D019221 Mandatory Reporting SCDO:0300009 Making information permanently non-identifiable that is associated with the identity of specific entities via encryption or other methods. Suggest update to description in MESH http://purl.bioontology.org/ontology/MESH/D000068240 Suggest update to description MESH:D000068240 Data De-Identification Data Masking De-Identification Data Anonymization SCDO:1000000 An observable characteristic of disease that has a severe and rapid onset of symptoms with short duration. Request inclusion into relevant ontology http://purl.obolibrary.org/obo/NCIT_C14140 http://semanticscience.org/resource/SIO_010056 None SCDO (Clair Ingram) Acute Phenotype SCDO:1000001 A unique identifier generated either manually or electronically when adding a subject to a study. deprecated Research Subject ID true SCDO:1000004 Procedures which temporarily or permanently remedy insufficient cleansing of body fluids by the kidneys. Could this and it's sub-classes not fall below any of the other main Therapeutics classes? Symptomatic? http://purl.bioontology.org/ontology/MESH/D017582 Sufficient SCDO:1000004 MESH:D017582 Renal Replacement Therapy SCDO:1000007 An abnormal hemoglobin caused by various point mutations within the HBB gene. This form of hemoglobin prevents red blood cells from carrying oxygen effectively. There are at least 8 different types of hemoglobin D. Request inclusion in the HPO, below "Abnormal Hemoglobin". Few but definitions not freely available Haemoglobin D Hb D HbD Hemoglobin D SCDO:1000008 A group of abnormal hemoglobins in which amino acid substitutions take place in either the alpha, beta or gamma chains but near the heme iron. This results in facilitated oxidation of the hemoglobin to yield excess methemoglobin which leads to cyanosis. Suggest update to description in MESH (to include "gamma chains") Suggest this term replaces "Methemoglobinemia" below "Abnormal Hemoglobin" in the HPO. http://purl.bioontology.org/ontology/MESH/D006449 Suggest update to description MESH:D006449 Hb M HbM Hemoglobin Hemoglobin M SCDO:1000009 An abnormal hemoglobin that results from the substitution of lysine for glutamic acid at position 26 of the beta chain. It is most frequently observed in southeast Asian populations. Request inclusion in the HPO, below "Abnormal Hemoglobin", for the sake of completion. http://purl.bioontology.org/ontology/MESH/D006446 Sufficient SCDO:1000009 MESH:D006446 Hb E Hemoglobin E SCDO:1000010 A group of disorders caused by large deletions of the beta-globin gene complex; typically 30% fetal haemoglobin. Request inclusion into relevant ontology http://ac.els-cdn.com/S014067361061029X/1-s2.0-S014067361061029X-main.pdf?_tid=691c25c0-5826-11e7-b704-00000aacb35e&acdnat=1498230953_4d1264c47385275daf8fc2a1e1de62e3 None HPFH-Sickle Cell Disease Syndrome Hereditary Persistence of Fetal Hemoglobin-Sickle Cell Disease Syndrome Sickle Cell Disease Syndrome-Hereditary Persistence of Fetal Hemoglobin Sickle Cell Disease-S/Persistence of Fetal Hemoglobin Sickle Cell-Hereditary Persistence of Fetal Hemoglobin Sickle Cell Disease-S/HPFH SCDO:1000012 Members of the beta-globin family. In humans, they are encoded in a gene cluster on chromosome 11. They include hemoglobin subunit epsilon, hemoglobin subunit gamma, hemoglobin subunit delta and hemoglobin subunit beta. There is also a pseudogene of beta (theta-beta) in the gene cluster. Adult hemoglobin is comprised of two alpha globin chains and two beta-globin chains. Sufficient SCDO:1000012 MESH:D055544 Beta-Globins Beta-Globin Family Members SCDO:1000013 This gene encodes the hemoglobin subunit beta and is located on chromosome 11 mapped at 11p15.5. Request inclusion into relevant ontology Negligable NCBIGene:3043 Beta-Globin Gene HBB Gene HBB1 Hemoglobin Beta Gene Hemoglobin Beta Locus Hemoglobin Subunit Beta Gene HBB SCDO:1000014 This gene encodes the hemoglobin subunit delta, which is a component of hemoglobin A2, which plays a role in the transport of oxygen to tissues of the adult body, but exists only in small amounts in all adult humans (1.5-3.1% of all hemoglobin molecules). Suggest update to description in NCIT http://purl.obolibrary.org/obo/NCIT_C84961 Suggest update to description NCIT:C84961 HBD Gene Hemoglobin Delta Gene Hemoglobin Subunit Delta Gene HBD SCDO:1000016 An abnormal hemoglobin that results from the substitution of glutamic acid with lysine at position 121 of the beta chain. Request inclusion in the HPO, below "Abnormal Hemoglobin". MESH and Zimmerman SA. Am J Hematol. 1999 Apr; 60(4) 279-84 Few but definitions not freely available Hb O-Arab Hb-Arab Hemoglobin-Arab Hemoglobin O-Arab SCDO:1000017 A material processing technique that uses operative manual and instrumental techniques on a patient to investigate and/or treat a pathological condition such as disease or injury or to help improve bodily function or appearance. http://purl.obolibrary.org/obo/ERO_0000378 Sufficient SCDO:1000017 ERO:0000378 Surgery SCDO:1000020 Treatment of factors associated with the definitive onset of a disease, illness, accident, behavioral response, or course of action. Usually one factor is more important or more obviously recognizable than others, if several are involved, and one may often be regarded as necessary. Examples include exposure to specific disease; amount or level of an infectious organism, drug, or noxious agent, etc. Request inclusion into relevant ontology http://purl.bioontology.org/ontology/MESH/D015985 None SCDO Management of Precipitating Factors Management of Underlying Cause Treatment of Underlying Cause Treatment of Precipitating Factors SCDO:1000023 'Every annotation must be attributed to a source, which may be a literature reference, another database or a computational analysis. The annotation must indicate what kind of evidence is found in the cited source to support the association between the gene product and the GO term. A simple controlled vocabulary is used to record evidence; and the evidence codes are simply the three-letter codes used to signify the type of evidence cited. [Curator team: Exact []]' The information in this class and its sub-classes will be migrated to evidence code properties. http://www.geneontology.org/faq/what-evidence-code obsolete Evidence Code true SCDO:1000024 'Used for annotations that depend directly on computation or automated transfer of annotations from a database, particularly when the analysis is performed internally and not published. A key feature that distinguishes this evidence code from others is that it is not made by a curator; use IEA when no curator has checked the specific annotation to verify its accuracy. [Curator team: Exact []]' http://geneontology.org/page/automatically-assigned-evidence-codes obsolete IEA (inferred from electronic annotation) true SCDO:1000025 'This should be used for information extracted from articles in the medical literature. [Curator team: []]' obsolete PCS (published clinical study) true SCDO:1000026 'Can be used for annotations based on individual clinical experience. [Curator team: []]' obsolete ICE (individual clinical experience) true SCDO:1000027 'Not described [Curator team: []]' obsolete ITM (inferred by text-mining) true SCDO:1000028 'Usually reviews or disease entries (e.g. OMIM) that only refers to the original publication. [Curator team: []]' obsolete TAS (traceable author statement) true SCDO:1000029 'used in all cases where the author makes a statement that a curator wants to capture but for which there are neither results presented nor a specific reference cited in the source used to make the annotation. [Curator team: []]' http://www.geneontology.org/page/nas-non-traceable-author-statement obsolete NAS (non-traceable author statement) true SCDO:1000030 'Used for those cases where an annotation is not supported by any direct evidence, but can be reasonably inferred by a curator from other annotations, for which evidence is available. [Curator team: []]' http://www.geneontology.org/page/ic-inferred-curator obsolete IC (inferred by curator) true SCDO:1000031 Terms deprecated in the "Personal Attribute" class. from personal attribute SCDO:1000032 A diagnostic instrument, technique, laboratory assay or test, or method of patient examination used for differential diagnosis. Request inclusion into relevant ontology. None SCDO (Jade Hotchkiss) Diagnostic Tool SCDO:1000033 A research instrument consisting of a series of questions and other prompts for the purpose of gathering information from respondents to assist with differential diagnosis. Request inclusion into relevant ontology http://en.wikipedia.org/wiki/Questionnaire Few but definitions not freely available Diagnostic Questionnaire Diagnostic Instrument SCDO:1000034 Terms deprecated in the "Diagnostics" class. from diagnostics SCDO:1000035 Terms deprecated in the "Therapeutics" class. from therapeutics SCDO:1000036 When the abnormal hemoglobin, hemoglobin C (HbC), has been detected in a blood sample. Few but definitions not available SCDO (Jade Hotchkiss) Haemoglobin C Present Haemoglobin C in Blood HbC Present HbC in Blood Hemoglobin C in Blood Hemoglobin C Present SCDO:1000037 An abnormality of the cerebral vasculature. Few but definitions not available HP:0100659 Abnormality of the Cerebral Blood Vessels Cerebrovascular Disorder Abnormality of the Cerebral Vasculature SCDO:1000038 A mutation wholly or partly responsible for causing a sickle cell disease. Request inclusion into relevant ontology B-Thal mutations: -- http://onlinelibrary.wiley.com/doi/10.1111/j.1582-4934.2004.tb00278.x/pdf -- https://www.ncbi.nlm.nih.gov/pubmed/15153712 None SCDO (Jade Hotchkiss) SCD Causal Mutation SCDO:1000039 The glutamic acid in position 6 in the primary sequence of a beta-chain produced by the HBB gene is replaced by valine. Request inclusion into relevant ontology http://www.bloodjournal.org/content/bloodjournal/46/3/363.full.pdf?sso-checked=true Negligable Beta S Mutation E6V Glu6Val Sickle Cell Mutation HBB, GLU6VAL SCDO:1000040 A mutation where the glutamic acid in position 121 in the primary sequence of a beta-chain produced by the HBB gene is replaced by lysine. This mutation is found as a single alteration in Hemoglobin O-Arab and is one of the two contributing mutations to the production of Hemoglobin S-Oman. Request inclusion into relevant ontology Negligable SCDO (Jade Hotchkiss) Beta O-Arab Mutation Contributing Beta S-Oman Mutation Glu121Lys HBB, GLU121LYS SCDO:1000041 A mutation where the glutamic acid in position 6 in the primary sequence of a beta-chain produced by the HBB gene is replaced by lysine. This mutation results in the production of Hemoglobin C and confers resistance to malaria. Request inclusion into relevant ontology Negligable SCDO (Jade Hotchkiss) Beta C mutation HbC Mutation HBB, GLU6LYS SCDO:1000042 A mutation in the HBB gene causing substitution of glutamic acid for lysine at the 26th position of the beta-globin chain. Request inclusion into relevant ontology Negligable SCDO (Jade Hotchkiss) Beta E Mutation HbE Mutation HBB, GLU26LYS SCDO:1000043 A person's concept of self as being male and masculine or female and feminine, or ambivalent, based in part on physical characteristics, parental responses, and psychological and social pressures. It is the internal experience of gender role. Sufficient SCDO:1000043 MESH:D005783 Gender Identity SCDO:1000044 A mutation where the aspartic acid in position 73 in the primary sequence of a beta-chain produced by the HBB gene is replaced by asparagine. This mutation is found as a single alteration in Hemoglobin Korle Bu and is one of the two contributing mutations to the production of Hemoglobin C-Harlem. Request inclusion into relevant ontology http://www.bloodjournal.org/content/bloodjournal/46/3/363.full.pdf?sso-checked=true Negligable SCDO (Jade Hotchkiss) Asp73Asn D73N HBB, ASP73ASN SCDO:1000045 A mutation where the valine in position 23 in the primary sequence of a beta-chain produced by the HBB gene is replaced by isoleucine. When compounded with the HbS mutation in the same gene, the sickling Hemoglobin S-Antilles is produced. Request inclusion into relevant ontology Negligable SCDO (Jade Hotchkiss) Contributing Beta S-Antilles Mutation Contributing Hb S-Antilles Mutation HBB, VAL23ILE SCDO:1000046 A mutation where the threonine in position 87 in the primary sequence of a beta-chain produced by the HBB gene is replaced by isoleucine. This mutation is found as a single alteration in Hemoglobin Quebec-Chori. Compound heterozygosity for Hb Quebec-chori and Hb S results in sickle cell disease. Request inclusion into relevant ontology Witkowska, H. E., Lubin, B. H., Beuzard, Y., Baruchel, S., Esseltine, D. W., Vichinsky, E. P., Kleman, K. M., Bardakdjian-Michau, J., Pinkoski, L., Cahn, S., Roitman, E., Green, B. N., Falick, A. M., Shackleton, C. H. L. Sickle cell disease in a patient with sickle cell trait and compound heterozygosity for hemoglobin S and hemoglobin Quebec-Chori. New Eng. J. Med. 325: 1150-1154, 1991. Negligable SCDO (Jade Hotchkiss) Hb Quebec-Chori Mutation HBB, THR87ILE SCDO:1000047 A mutation where the leusine residue in position 6 in the primary sequence of a beta-chain produced by the HBB gene is replaced by phenylalanine. This mutation on its own produces a stable hemoglobin that does not result in hemolysis (Hb Rockford), but when in combination with the Hb S mutation (HBB, GLU6VAL), the symptomatic Hb Jamaica Plain is produced. Request inclusion into relevant ontology Perrault, J., Fairbanks, V. F., McCormick, D. J., Kubik, K., Madden, B. J., Holmes, M. W., Hoyer, J. D. Hemoglobin Rockford, beta68(E12)leu-to-phe: a new HB variant associated with mild anemia. (Abstract) Blood 90 (Suppl. 1): 30b, 1997. Negligable SCDO (Jade Hotchkiss) Contributing Hb Jamaica Plain Mutation HBB, LEU68PHE SCDO:1000048 The alleles, or variant forms of the HBB gene, that are carried by an SCD sufferer. Probably too specific to be included in other ontologies. Paper mentioning haplotypes and severity: -- https://www.nature.com/scitable/topicpage/sickle-cell-anemia-a-look-at-global-8756219 -- -- Table of SCD Genotypes: -- http://onlinelibrary.wiley.com/doi/10.1111/j.1582-4934.2004.tb00278.x/pdf -- -- HBB allelic variants: -- https://www.omim.org/entry/141900#0243 -- -- Perhaps have parent class Hemoglobinopathy Genotype, with Hemoglobinopathy Trait below that? http://www.nature.com/scitable/definition/genotype-234 None SCDO (Jade Hotchkiss) Sickle Cell Disease Genotype Sickle Genotype SCD Genotype SCDO:1000049 The genotype when an individual has the Hb C gene from one parent and the Hb S gene from the other. Individuals with Hb SC have similar symptoms to individuals with Hb SS, however, the anemia is less severe. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) Haemoglobin Genotype SC SC Genotype beta6Glu>Val/beta6Glu>Lys Hemoglobin Genotype SC SCDO:1000050 Compound heterozygosity for the hemoglobin S (HBB Glu6Val) and hemoglobin D-Punjab (HBB Glu121Gln) variants. Hemoglobin Genotype S/D-Punjab Torres LS, Okumura JV, Silva DG, Bonini-Domingos CR. Hemoglobin D-Punjab: origin, distribution and laboratory diagnosis. Rev Bras Hematol Hemoter. 2015;37(2): 120–126. pmid:25818823 None Haemoglobin Genotype S/D-Punjab S/D-Punjab Genotype beta6Glu>Val/beta121Glu>Gln Hemoglobin Genotype S/D-Punjab SCDO:1000051 Compound heterozygosity for the hemoglobin S (HBB Glu6Val) and hemoglobin O-Arab (HBB GluU121Lys) variants. Request inclusion into relevant ontology Lancet. 2010 Dec 11;376(9757):2018-31. doi: 10.1016/S0140-6736(10)61029-X. Epub 2010 Dec 3. None Haemoglobin Genotype S/OArab S/O-Arab Genotype beta6Glu>Val/beta121Glu>Lys Hemoglobin Genotype S/O-Arab SCDO:1000052 Compound heterozygosity for the hemoglobin S (HBB Glu6Val) and hemoglobin E (HBB Glu26Lys) variants. Request inclusion into relevant ontology Lancet. 2010 Dec 11;376(9757):2018-31. doi: 10.1016/S0140-6736(10)61029-X. Epub 2010 Dec 3. None Haemoglobin Genotype SE SE Genotype SE Hemoglobin Genotype beta6Glu>Val/beta26Glu>Lys Hemoglobin Genotype SE SCDO:1000053 The homozygous genotype that involves a substitution of glutamic acid for a valine at position 6 of beta-globin chains produced by both beta-globin gene (HBB) alleles. Request inclusion into relevant ontology Few but definitions not specific enough SCDO (Jade Hotchkiss) Haemoglobin Genotype SS Hemoglobin S Genotype SS Genotype beta6Glu>Val/beta6Glu>Val Hemoglobin Genotype SS SCDO:1000054 Compound heterozygous inheritance of Hb S and Hb D mutations. Hb S occurs from substitution of valine for glutamic acid in the beta-6 position (beta6Glu>Val). Hb D generally results from substitution of glutamic acid for glutamine at beta-121 (beta121Glu>Gln); such as the Hb D-Punjab/Hb D-Los Angeles variants. There are several other Hb D variants, including Hb D-Iband where threonine is substituted by lysine at beta-87 (beta87Thr>Lys) and Hb D-Iran where glutamic acid is substituted by glutamine at beta-22 (beta22Glu>Gln). Request inclusion into relevant ontology None SCDO Haemoglobin Genotype SD SD Genotype Hemoglobin Genotype SD SCDO:1000056 Compound heterozygous inheritance of Hb S and Hb C-Harlem mutations. Hb S occurs from substitution of valine for glutamic acid in the beta-6 position (beta6Glu>Val). Hb C-Harlem involves two substitutions in each beta-chain: the first being identical to that found in Hb S, and the second being a substitution of aspartic acid at position 73 by asparagine (beta73Asp>Asn). Request inclusion into relevant ontology PMID: 1148394 None SCDO Haemoglobin Genotype S/C-Harlem S/C-Harlem Genotype beta6Glu>Val/beta6Glu>Val, beta73Asp>Asn Hemoglobin Genotype S/C-Harlem SCDO:1000058 An abnormal hemoglobin in which two mutations occur in its beta-chains results in the sickling of red blood cells containing this hemoglobin. The sickling is the result of the mutation in which glutamic acid in position 6 is replaced by valine, which is not counteracted by the second mutation, in which the aspartic acid in position 73 is replaced by asparagine. Request inclusion into the HPO, below "Abnormal Hemoglobin"/"Sickling Hemoglobin with Two Beta-Globin Gene Substitutions". https://www.omim.org/entry/141900#0243 Few but definitions not freely available SCDO (Jade Hotchkiss) HbS-HBC-Harlem Hemoglobin C-Georgetown Hemoglobin S-Hemoglobin C-Harlem Hemoglobin C-Harlem SCDO:1000059 The inheritance of the gene for hemoglobin D-Punjab from one parent and a gene for normal adult hemoglobin (hemoglobin A) from the other parent. Request inclusion into NCIT below "Hemoglobin Trait". None SCDO (Jade Hotchkiss) Hb AD-Punjab Hemoglobin D-Punjab Trait causes no clinical or hematological alterations Hemoglobin D-Punjab Trait SCDO:1000060 The underlying molecular makeup resulting in sickle cell disease. Probably too specific to warrant inclusion into anther ontology. Consider inclusion of other sub-classes of this term in the Human Phenotype Ontology. -- - Elevated hemoglobin A1c -- - Imbalanced Hemoglobin Synthesis (and the 2 terms below this) -- Methemoglobina -- Others from MESH?: -- J, M, Methemoglobin? None SCDO (Clair Ingram) SCD Molecular Phenotype SCDO:1000061 An altered level of normal hemoglobin (Hemoglobin A (Hb A), Hemoglobin A2 (Hb A2) or Hemoglobin F (Hb F, fetal hemoglobin) in the blood, which may be seen in those suffering with Sickle Cell Disease (SCD). Probably too specific to SCD be included in other ontologies. None SCDO (Jade Hotchkiss) Altered Level of Normal Hemoglobin in SCD SCDO:1000062 A rare type of sickle cell disease with the compound heterozygous genotype involving the mutations for Hemoglobin S and Hemoglobin C-Harlem. This condition is described to have a clinical course similar to sickle cell anemia. Request inclusion into relevant ontology Moo-Penn, W., Bechtel, K., Jue, D., Chan, M.S., Hopkins, G., Schneider, N.J., Wright, J. and Schmidt, R.M., 1975. The presence of hemoglobin S and C Harlem in an individual in the United States. Blood, 46(3), pp.363-367. None SCDO (Clair Ingram) SC(Harlem) Disease Sickle Cell-Hemoglobin C-Harlem Disease Sickle Cell Disease-S/C-Harlem SCDO:1000063 A 106-kb deletion of the beta globin gene cluster. Request inclusion into relevant ontology Negligable SCDO (Jade Hotchkiss) HPFH1 HBB, 106-KB DEL SCDO:1000064 A consent model in which participants are given a set of options allowing them to select how they want to participate in the research. Request inclusion into the Informed Consent Ontology. https://www.genome.gov/27559022/informed-consent-glossary/ None Tiered Consent SCDO:1000065 Requires that consent to the use of human samples be specific to the 'purpose' for which the sample is to be used and that where previously collected samples are to be used for a different 'research purpose' further consent should generally be obtained. Request inclusion into the ICO below "Informed Consent". https://www.alrc.gov.au/publications/15-human-genetic-research-and-consent/specific-consent None SCDO Specific Consent SCDO:1000066 The determination of the amount of hemoglobin F present in a sample. Suggest update to label in NCIT (from "Hemoglobin F Measurement") Add sub-classes of "Fetal hemoglobin determination" in SNOMED CT? Suggest update to label NCIT:C92262 Fetal Hemoglobin Test HGBF Test Hemoglobin F Test SCDO:1000067 When one beta-globin gene carries the hemoglobin S mutation (beta6Glu>Val) whereas the other carries a null mutation, called beta-zero, because of the resulting inability to synthesize any beta-globin chain. Request inclusion into relevant ontology None S/Beta-Zero-Thal Genotype S/Beta-Zero-Thalassaemia Genotype S/Beta-Zero-Thalassemia Hemoglobin Genotype S/Beta Zero Thalassaemia SCDO:1000068 'Genotype where a person is a compound heterozygote for the hemoglobin S mutation and a severe beta plus thalassemia mutation. Source: CLAIR [Curator team: []]' Rees, D.C., Williams, T.N. and Gladwin, M.T., 2010. Sickle-cell disease. The Lancet, 376(9757), pp.2018-2031. Severe S/Beta-Plus-Thal Severe S/Beta-Plus-Thal Genotype Severe S/Beta-Plus-Thalassaemia Genotype deprecated Severe S/Beta-Plus-Thal true SCDO:1000069 Genotype whereby a person is heterozygous for a hemoglobin S mutation and heterozygous for a mutation that causes persistant fetal hemoglobin production into adulthood. HPFH causative mutations are largely due to deletions in the beta-globin locus, but also by point mutations in the gamma-globin gene promoters. Request inclusion into relevant ontology Stamatoyannopoulos, G. (2005). Control of globin gene expression during development and erythroid differentiation. Experimental Hematology, 33(3), 259. http://doi.org/10.1016/j.exphem.2004.11.007 None SCDO (Clair Ingram) Haemoglobin Genotype S/HPFH S/HPFH Genotype Hemoglobin Genotype S/HPFH SCDO:1000070 A compound heterozygous genotype, involving the mutations for Hemoglobin S (beta6Glu>Val) and Hemoglobin Lepore Boston. Request inclusion into relevant ontology PMID: 7055103 Stevens MC, Lehmann H, Mason KP, Serjeant BE, Serjeant GR. 1982. Sickle cell Hb Lepore Boston syndrome. Uncommon differential diagnosis to homozygous sickle cell disease. Am J Dis Child. 136(1):19-22. None Haemoglobin Genotype S/Lepore S/Lepore S/Lepore Boston Genotype S/Lepore Genotype Hemoglobin Genotype S/Lepore Boston SCDO:1000071 A genotype that involves a double mutation in one beta-globin gene that results in hemoglobin with low oxygen affinity, which results in the polymerisation of the hemoglobin variant (hemoglobin Jamaica Plain) and thus sickling of erythorcytes. Request inclusion into relevant ontology http://ac.els-cdn.com/S014067361061029X/1-s2.0-S014067361061029X-main.pdf?_tid=691c25c0-5826-11e7-b704-00000aacb35e&acdnat=1498230953_4d1264c47385275daf8fc2a1e1de62e3 None A/Jamaica Plain Genotype A/Jamaica Plain Haemoglobin Genotype A/Jamaica Plain Hemoglobin Genotype Haemoglobin Genotype A/Jamaica Plain Hemoglobin Genotype A/Jamaica Plain SCDO:1000072 A sickling hemoglobin with reduced oxygen affinity that causes severe hemolytic anemia and sickling of erythrocytes. Request inclusion into the HPO, below "Abnormal Hemoglobin"/"Sickling Hemoglobin with Two Beta-Globin Gene Substitutions". http://www.nejm.org/doi/full/10.1056/NEJMoa040771#t=article None SCDO (Jade Hotchkiss) Hb JP Hb Jamaica Plain Hemoglobin JP Hemoglobin Jamaica Plain SCDO:1000073 A form of hemoglobin caused by two mutations in its beta-chains, the classic beta S mutation (beta 6 Glu>Val) and beta 23 Val>Ile. Hemoglobin S-Antilles has the same electrophoretic mobility as Hemoglobin S but a distinct isoelectric focus and produces sickling in the carriers of the Hb A/S Antilles trait. Request inclusion into the HPO, below "Abnormal Hemoglobin"/"Sickling Hemoglobin with Two Beta-Globin Gene Substitutions". Few but definitions not freely available SCDO (Jade Hotchkiss) Hemoglobin S-Antilles SCDO:1000074 A form of hemoglobin caused by two mutations in a beta-globin chain, the classic beta S mutation (beta6 Glu> Val) and a beta121 Glu > Lys mutation identical to that of Hb-O Arab. The hemoglobin variant has reduced solubility and there is an apparent increase in red cell sickling tendency. It is reported to cause a rare dominant form of sickle cell disease, Sickle Cell Disease A/S-Oman. Request inclusion into the HPO, below "Abnormal Hemoglobin"/"Sickling Hemoglobin with Two Beta-Globin Gene Substitutions". Nagel, R.L., Daar, S., Romero, J.R., Suzuka, S.M., Gravell, D., Bouhassira, E., Schwartz, R.S., Fabry, M.E. and Krishnamoorthy, R., 1998. HbS-Oman heterozygote: a new dominant sickle syndrome. Blood, 92(11), pp.4375-4382. Negligable SCDO (Jade Hotchkiss) Hb S-Oman Hemoglobin S (Oman) Hemoglobin S-Oman SCDO:1000075 Dominant heterozygosity for the double HBB Glu6Val and Glu121Lys mutation. Request inclusion into relevant ontology PMID: 9834244 None A/S-Oman Genotype A/S-Oman Haemoglobin Genotype A/S-Oman Hemoglobin Genotype Haemoglobin Genotype A/S-Oman Hemoglobin Genotype A/S-Oman SCDO:1000076 A form of sickle cell thalassemia, with a mild clinical phenotype, characterized by the presence of hemoglobin S and a small amount of hemoglobin A in the red blood cells. Request inclusion into relevant ontology Rees, D.C., Williams, T.N. and Gladwin, M.T., 2010. Sickle-cell disease. The Lancet, 376(9757), pp.2018-2031. None SCDO (Clair Ingram) Mild Sickle Cell Disease-S Beta Minus Thalassaemia Mild Sickle Cell-Beta Minus Thalassaemia Mild Sickle Cell-Beta Minus Thalassemia Mild Sickle Cell Disease-S Beta Minus Thalassemia SCDO:1000077 A form of sickle cell thalassemia, with a moderate clinical phenotype, characterized by the presence of hemoglobin S and a small amount of hemoglobin A in the red blood cells. Request inclusion into relevant ontology Rees, D.C., Williams, T.N. and Gladwin, M.T., 2010. Sickle-cell disease. The Lancet, 376(9757), pp.2018-2031. None SCDO (Clair Ingram) Moderate Sickle Cell Disease-S Beta Minus Thalassaemia Moderate Sickle Cell-Beta Minus Thalassaemia Moderate Sickle Cell-Beta Minus Thalassemia Moderate Sickle Cell Disease-S Beta Minus Thalassemia SCDO:1000078 A form of sickle cell thalassemia, with a severe clinical phenotype, characterized by the presence of hemoglobin S and a small amount of hemoglobin A in the red blood cells. Request inclusion into relevant ontology Rees, D.C., Williams, T.N. and Gladwin, M.T., 2010. Sickle-cell disease. The Lancet, 376(9757), pp.2018-2031. None SCDO (Clair Ingram) Severe Sickle Cell Disease-S Beta Minus Thalassaemia Severe Sickle Cell-Beta Minus Thalassaemia Severe Sickle Cell-Beta Minus Thalassemia Severe Sickle Cell Disease-S Beta Minus Thalassemia SCDO:1000079 'Genotype where a person is a compound heterozygote for the hemoglobin S mutation and a moderate beta plus thalassemia mutation. Source: CLAIR [Curator team: []]' Rees, D.C., Williams, T.N. and Gladwin, M.T., 2010. Sickle-cell disease. The Lancet, 376(9757), pp.2018-2031. Moderate S/Beta-Plus-Thalassaemia deprecated Moderate S/Beta-Plus-Thal true SCDO:1000080 'Not described [Curator team: []]' Mild S/Beta-Plus-Thalassaemia deprecated Mild S/Beta-Plus-Thal true SCDO:1000081 Compound heterozygosity for the hemoglobin C (HBB Glu6Lys) mutation and the double HBB Glu6Val, Val23Ile mutation of hemoglobin S-Antilles. Request inclusion into relevant ontology DOI: 10.1016/S0140-6736(10)61029-X PMID: 21131035 None C/S Antilles Genotype C/S Antilles Haemoglobin Genotype C/S Antilles Hemoglobin Genotype Haemoglobin Genotype C/S Antilles beta6Glu>Lys/beta6Glu>Val, beta23Val>Ile Hemoglobin Genotype C/S Antilles SCDO:1000082 A hemoglobin that sickles due to the presence of two beta-globin gene mutations within the same HBB gene. Request inclusion into the HPO, below "Abnormal Hemoglobin". None Doubly Substituted Sickling Hemoglobin Sickling Hemoglobin with Two Beta-Globin Gene Substitutions SCDO:1000083 An abnormal hemoglobin in which two mutations occurring in its beta-chains results in the sickling of red blood cells containing this hemoglobin. The sickling is the result of the mutation in which glutamic acid in position 6 is replaced by valine, which is not counteracted by the second mutation, in which the lysine in position 132 is replaced by asparagine. Request inclusion into the HPO, below "Abnormal Hemoglobin"/"Sickling Hemoglobin with Two Beta-Globin Gene Substitutions". Luo, H.Y., Adewoye, A.H., Eung, S.H., Skelton, T.P., Quillen, K., McMahon, L., Steinberg, M.H. and Chui, D.H., 2004. A novel sickle hemoglobin: Hemoglobin S-South End. Journal of pediatric hematology/oncology, 26(11), pp.773-776. Negligable SCDO (Jade Hotchkiss) Hemoglobin S-South End SCDO:1000084 A compound heterozygous genotype, involving the mutations for Hemoglobin S and Hemoglobin Quebec Chori, which shows an electrophoretic pattern similar to that of the Hb A/S Genotype, but shows sickling. Request inclusion into relevant ontology Pediatr Blood Cancer. 2007 Aug;49(2):207-10. None SCDO Haemoglobin Genotype S/Quebec-Chori S/Quebec-Chori Genotype beta6Glu>Val/beta87Thr>Ile Hemoglobin Genotype S/Quebec-Chori SCDO:1000085 An abnormal hemoglobin in which a threonine is replaced by an isoleucine residue at the eighty-seventh position of beta chains. It migrates like HbA but promotes sickling. Suggest update to description in MESH (the term in MESH doesn't currently have a description). Also request inclusion in the HPO, below "Abnormal Hemoglobin", for the sake of completion. Witkowska, H.E., Lubin, B.H., Beuzard, Y., Baruchel, S., Esseltine, D.W., Vichinsky, E.P. et al. Sickle cell disease in a patient with sickle cell trait and compound heterozygosity for hemoglobin S and hemoglobin Quebec-Chori. N Engl J Med. 1991; 325: 1150–1154 Suggest update to description http://ac.els-cdn.com/S014067361061029X/1-s2.0-S014067361061029X-main.pdf?_tid=691c25c0-5826-11e7-b704-00000aacb35e&acdnat=1498230953_4d1264c47385275daf8fc2a1e1de62e3 MESH:C070823 Hb Quebec-Chori Hemoglobin Quebec Chori SCDO:1000086 A severe compound heterozygous sickling disorder characterized by the presence of both hemoglobin S and hemoglobin Quebec Chori. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) Sickle Cell-Hemoglobin Quebec Chori Disease Sickle Cell Disease-S/Quebec Chori SCDO:1000087 A mutation where the lysine residue in position 132 in the primary sequence of a beta-chain produced by the HBB gene is replaced by asparagine. This mutation on its own produces Hb Yamagata which has reduced oxygen affinity, but no distinctive clinical abnormalities. However, when present in the same gene as the Hb S mutation (HBB, GLU6VAL), the sickling HbS-South End is produced. Request inclusion into relevant ontology Negligable SCDO (Jade Hotchkiss) Contributing Beta S-South End Mutation Contributing Hb S-South End Mutation Hb Yamagata Mutation LYS132ASN HBB, LYS132ASN SCDO:1000088 A compound heterozygous genotype, involving the mutations for hemoglobin S and hemoglobin S-South End. Request inclusion into relevant ontology None Haemoglobin Genotype S/S-South End S/S-South End Genotype beta Glu6Val, GAG>GTG/beta Glu6Val, GAG>GTG; beta Lys132Asn, AAA>AAC beta6Glu>Val/beta132Lys>Asn Hemoglobin Genotype S/S-South End SCDO:1000089 The most common Hemoglobin Lepore type and the only type of the three known variants described in association with HbS. This abnormal hemoglobin consists of two normal alpha globin chains (HBA) and two deltabeta globin fusion chains which occur due to a crossover between the delta (HBD) and beta globin (HBB) gene loci during meiosis. Suggest inclusion in the HPO, below "Abnormal Hemoglobin". Hb Lepore is produced at a reduced rate and this is why the disease is related to the Β-thalassemic syndromes. Quantity in heterozygotes 7-13%; found in combination with Hb S, Hb C, beta+-thal, and in the homozygous state. The most common Hb Lepore type; found mainly in Italian families; it has also been observed in families from Rumania, Yugoslavia, Turkey, Cyprus, Jamaica, Cuba, Greece, England, Australia, Mexico, etc http://en.wikipedia.org/wiki/Hemoglobin_Lepore_syndrome#Homozygous_Hb_Lepore http://globin.cse.psu.edu/html/huisman/variants/hybrid/Lepore-Boston-Washington.html Few but definitions not freely available Hb Lepore Boston-Washington Hb Lepore-B-W Hb Lepore-Boston-Washington Hb Lepore-WB Hb Lepore-Washington-Boston Hemoglobin Lepore Boston-Washington Hemoglobin Lepore-Boston-Washington Hemoglobin Lepore Boston SCDO:1000090 A rare, reported severe, type of sickle cell disease with the compound heterozygous genotype involving the mutations for Hemoglobin S and Hemoglobin S-South End. Request inclusion into relevant ontology Luo, H.Y., Adewoye, A.H., Eung, S.H., Skelton, T.P., Quillen, K., McMahon, L., Steinberg, M.H. and Chui, D.H., 2004. A novel sickle hemoglobin: Hemoglobin S-South End. Journal of pediatric hematology/oncology, 26(11), pp.773-776. None SCDO (Clair Ingram) Sickle Cell-Hemoglobin S-South End Disease Sickle Cell Disease-S/S-South End SCDO:1000091 'Sb+ thalassemia is an inherited condition. Hemoglobin S comes from one parent and Beta plus thalassemia comes from the other parent. Instead of appearing round (like donuts), red blood cells are somewhat small, pale and misshapen. [Curator team: []]' deprecated Sickle beta plus thalassemia true SCDO:1000092 A primary headache disorder that is characterized by severe, strictly unilateral PAIN which is orbital, supraorbital, temporal or in any combination of these sites, lasting 15-180 min. occurring 1 to 8 times a day. The attacks are associated with one or more of the following, all of which are ipsilateral: conjunctival injection, lacrimation, nasal congestion, rhinorrhea, facial SWEATING, eyelid EDEMA, and miosis. Ask a clinician if this is different to a cluster headache? https://meshb.nlm.nih.gov/record/ui?ui=D003027 MESH:D003027 deprecated-Acute Severe Headache true SCDO:1000093 A medically undesirable event occurring in a research subject, such as an abnormal sign, symptom, worsening of a disease, injury, etc. A serious adverse event (SAE) results in death, hospitalization (or increased hospital stay), persistent disability, birth defect, or any other outcome that seriously jeopardizes the subject's health. Sufficient SCDO:1000093 OAE:0000001 Adverse Reaction Adverse Event (AE) SCDO:1000094 A desirable research outcome or state of affairs, such as medical treatment, clinically useful information, or self-esteem. In the oversight of human subjects research, money is usually not treated as a benefit. Request inclusion into relevant ontology Shamoo AE and Resnik DB, Responsible Conduct of Research, 3rd ed. (New York: Oxford University Press, 2015). None SCDO Research Benefit SCDO:1000095 A situation in which an individual or their close associates might benefit personally from official or professional actions. It includes a conflict between a person's private interests and official responsibilities in a position of trust.The concept refers both to actual conflict of interest and the appearance or perception of conflict. http://purl.bioontology.org/ontology/MESH/D016265 Few but definitions not specific enough MESH:D016265 Interest Conflict Conflict of Interest SCDO:1000097 An homo sapiens that bears an experimental subject role which is realized through his/her participation in a scientific technique as the subject of interest (ie as the subject about which data is generated in an assay or study, or the entity that is transformed or modified in a material processing technique). Sufficient SCDO:1000097 ERO:0001964 Human Subject SCDO:1000098 A paper or electronic questionnaire specifically used in research by the sponsor of the research to collect data from each research participant. All data on each participant in the study are held and/or documented in the CRF, including adverse events. Request inclusion into relevant ontology, perhaps as parent of "electronic case report form" in the Ontology for Biomedical Investigations (OBI) Debbie Kennedy, CRF Designer, Canary Publications, ISBN 0-9531174-7-2 None SCDO Case Report Form (CRF) SCDO:1000099 Genes with alleles that affect the phenotype associated with a nonallelic gene. Sufficient SCDO:1000099 MESH:D060045 Gene, Modifier Modifier Gene SCDO:1000100 The type of ICD-10-CM code, in terms of a code's usability for reimbursement purposes. None SCDO (Jade Hotchkiss) ICD-10-CM Code Type SCDO:1000103 A specific region that is mapped within a genome. Genetic loci are usually identified with a shorthand notation that indicates the chromosome number and the position of a specific band along the P or Q arm of the chromosome where they are found. For example the locus 6p21 is found within band 21 of the P-arm of CHROMOSOME 6. Many well known genetic loci are also known by common names that are associated with a genetic function or hereditary disease. Sufficient SCDO:1000103 MESH:D056426 Genetic Loci Loci, Genetic Locus, Genetic Genetic Locus SCDO:1000104 The protein subunits that comprise multimeric hemoglobins. Sufficient SCDO:1000104 MESH:D055554 Hemoglobin Subunits SCDO:1000105 Members of the alpha-globin family. In humans, they are encoded in a gene cluster on chromosome 16. They include hemoglobin subunit zeta and hemoglobin subunit alpha. There are also pseudogenes of zeta (theta-zeta) and alpha (theta-alpha) in the cluster. Adult hemoglobin is comprised of 2 alpha-globin chains and 2 beta-globin chains. Sufficient SCDO:1000105 MESH:D055542 Alpha-Globins Alpha-Globin Family Members SCDO:1000106 Sickle cell disease (SCD) is a pleiotropic inherited disorder of the blood, characterised by the appearance of sickle-shaped red blood cells and anemia. It results from homozygosity for the sickle beta-globin gene mutation at position 6 (glu > val), or compound heterozygosity for the sickle gene and either another mutation for a different hemoglobin variant or one of numerous beta-thalassemia mutations. Suggest update to description in NCIT. Sickle cell diseases include inheritance of the gene for sickle hemoglobin from one parent and one of the following: A gene for sickle hemoglobin from the other parent (Hb SS), A gene for another abnormal hemoglobin from the other parent (Hb SC, HbSD Punjab, HbSO Arab, HbS Leopore, or Hb SE), A gene that limits hemoglobin production from the other parent (sickle beta +/0 thalassemia). In S beta (+) thalassemia there is some production of beta globin, and in S beta (0) thalassemia there is no production of beta globin. Few but definitions not specific enough Banana Cell Disease Drepanocytosis SCD Sickle Cell Disorder Sickle Cell Hemoglobinopathy Sickle Hemoglobinopathy Sickle-Cell Disorder Sickle Cell Disease SCDO:1000107 The combination of the hemoglobin S mutation (beta6Glu>Val) and a beta-thalassemia mutation. Request inclusion into relevant ontology None Hemoglobin Genotype S/Beta Thalassaemia S/Beta -Thal Genotype S/Beta -Thalassaemia Genotype Hemoglobin Genotype S/Beta Thalassemia SCDO:1000108 A mutation where the serine in position 9 in the primary sequence of a beta-chain produced by the HBB gene is replaced by tyrosine. This mutation is one of 2 amino acid substitutions in the same beta chain that produces the asymptomatic Hemoglobin D-Agri, the other mutation being HBB, GLU121GLN, which on its own produces Hemoglobin D-Punjab. Request inclusion into relevant ontology Negligable SCDO (Jade Hotchkiss) Beta D-Agri Mutation HBB, SER9TYR SCDO:1000109 A mutation where the glutamic acid in position 121 in the primary sequence of a beta-chain produced by the HBB gene is replaced by glutamine. Request inclusion into relevant ontology Negligable SCDO (Jade Hotchkiss) Beta 121Glu>Gln Beta D-Punjab Mutation Derived from a point mutation in the beta-globin gene (HBB: c.364G>C; rs33946267). HBB, GLU121GLN SCDO:1000110 A mutation where the glycine in position 16 in the primary sequence of a beta-chain produced by the HBB gene is replaced by arginine. Request inclusion into relevant ontology Negligable SCDO (Jade Hotchkiss) Beta D-Bushman Mutation HBB, GLY16ARG SCDO:1000111 A mutation where the asparargine acid in position 19 in the primary sequence of a beta-chain produced by the HBB gene is replaced by lysine. Request inclusion into relevant ontology Negligable SCDO (Jade Hotchkiss) Beta D-Ouled Rabah Mutation HBB, ASN19LYS SCDO:1000112 A mutation where the glutamic acid in position 22 in the primary sequence of a beta-chain produced by the HBB gene is replaced by glutamine. Request inclusion into relevant ontology Negligable SCDO (Jade Hotchkiss) Beta D-Iran Mutation HBB, GLU22GLN SCDO:1000113 A mutation where the glutamic acid in position 22 in the primary sequence of a beta-chain produced by the HBB gene is replaced by valine. Request inclusion into relevant ontology Negligable SCDO (Jade Hotchkiss) Beta D-Granada Mutation HBB, GLU22VAL SCDO:1000114 A mutation where the threonine in position 87 in the primary sequence of a beta-chain produced by the HBB gene is replaced by lysine. Request inclusion into relevant ontology Negligable SCDO (Jade Hotchkiss) Beta D-Ibadan Mutation HBB, THR87LYS SCDO:1000115 A mutation where the glutamic acid in position 121 in the primary sequence of a beta-chain produced by the HBB gene is replaced by alanine. Request inclusion into relevant ontology Negligable SCDO (Jade Hotchkiss) Beta D-Neath Mutation HBB, GLU121ALA SCDO:1000116 The Adja ethnic group are mostly farmers and live in the southern part of Benin Republic. They make up 15% of the general country population. This group of people migrated into Benin between the 12th and 13th centuries from River Mono. The primary language is Aja-Gbe with a majority of the people being trilingual. Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? Negigable Demographic and Health Surveys Program (2011-2012) Adja Ethnic Group Adja SCDO:1000117 Bariba is the ethnic group dominating the northern side of Benin, who constitute 9% of the population. They are the first inhabitants of Benin and are concentrated in the capital city, Nikki. One of their leading practices is horse riding, which is a practice that has been enjoyed from generation to generation. With agriculture being their dominant occupation, Bariba people have a diverse range of produce such as corn, rice and palm oil. Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? Negligable Demographic and Health Surveys Program (2011-2012) Bariba Ethnic Group Bariba SCDO:1000118 Negligable Dendi Ethnic Group Dendi SCDO:1000119 The largest ethnic group in Benin is Fon/Dahomey which constitutes 39% of the total population. Established in 1600 by the Fon, a group that came about through the intermarriage between the Adja and local Gedevi. Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? None Demographic and Health Surveys Program (2011-2012) Fon Ethnic Group Fon SCDO:1000120 None Yoa Ethnic Group Yoa SCDO:1000121 None Betamaribe Ethnic Group Betamaribe SCDO:1000122 The Embu are a Bantu-speaking people who are closely related to the Gikuyu of Ndia and Gicugu to the west, the Mbeere and the Kamba to the southeast, and the Chuka and the Meru to the north in Kenya. Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? Negligable Demographic and Health Surveys Program (2015) Embu Ethnic Group Embu SCDO:1000123 The Kalenjin ethnic group are one of the five largest ethnic groups in Kenya. They are a Nilotic ethnic group and they are mainly farmers. Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? None Demographic and Health Surveys Program (2015) Kalenjin Ethnic Group Kalenjin SCDO:1000124 The Kamba ethnic group, also known as Akamba is one of the five largest ethnic groups in Kenya. They are Bantu-speaking people and primarily agriculturists. Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? None Demographic and Health Surveys Program (2015) Kamba Ethnic Group Kamba SCDO:1000125 The Kikuyu are the largest single ethnic tribe in Kenya, making up 22% of the country's population. It is believed that the Kikuyu people migrated from Lake Chad to East Africa in 1000 AD, settling in the fertile central highlands of Kenya and engaging in farming. Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? Few but definitions not freely available Demographic and Health Surveys Program (2015) Kikuyu Ethnic Group Kikuyu SCDO:1000126 The Kisii tribe (also known as the Gusii tribe) is a Bantu ethnic group who occupy the Kisii highlands in Nyanza, Western Kenya. The Kisiis constitute the sixth largest ethnic group, comprising about seven percent of the national population. Kisii, which is their ethnic language, is also traditionally known as Ekegusii. Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? Few but definitions not specific enough Demographic and Health Surveys Program (2015) Gusii Kisii Ethnic Group Kisii SCDO:1000127 The Luhya ethnic group, also known as the Abaluhya, Baluhya, or Abaluyia, is a Bantu tribe living in Kenya's agriculturally fertile western region. They are the second largest tribe in Kenya and neighbors to some of the Nilotic tribes, including the Luo, Kalenjin, Maasai and Teso (Iteso). Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? None Demographic and Health Surveys Program (2015) Luhya Ethnic Group Luhya SCDO:1000128 Luo, also called Joluo or Kavirondo constitute the fourth largest ethnic group in Kenya. The Luo speak a Nilotic language of the Nilo-Saharan language family. Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? Few but definitions not freely available Demographic and Health Surveys Program (2015) Luo Ethnic Group Luo SCDO:1000129 A smaller ethnic group, accounting for only about 0.7 percent of Kenya's population, with a similar number living in Tanzania. Maasais speak Maa, a Nilotic ethnic language from their origin in the Nile region of North Africa. Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? None Demographic and Health Surveys Program (2015) Maasai Ethnic Group Maasai SCDO:1000130 None Peulh Ethnic Group Peulh SCDO:1000131 Yoruba is an ethnic group coming from Nigeria and well settled along the eastern boundary of Benin. They are more than 18% of the population. The majority of the Yoruba people in Benin are descendants of the Ife tribe, and the Yoruba people are predominantly of the Muslim religion. Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? Few but definitions not specific enough Demographic and Health Surveys Program (2011-2012) Yoruba Ethnic Group Yoruba SCDO:1000132 The Meru tribe or Merus is a Bantu ethnic group. They reside on Mount Kenya's agriculturally rich northeastern slopes, in Kenya's Eastern Province. The name Meru refers to both the people and the location. Merus are primarily agrarian, raising a few domestic animals. Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? Not relevant to context of sickle cell Demographic and Health Surveys Program (2015) Meru Ethnic Group Meru SCDO:1000133 The Mijikenda tribe is a Kenyan coastal Bantu tribe that consists of nine closely related sub-tribes. "Mijikenda" literally means nine homes or nine homesteads (in Swahili), referring to the common ancestry of the Mijikenda people. The nine Mijikenda sub-tribes are believed to be nine different homes of the same tribe. Each sub-tribe speaks its own dialect of the Mijikenda language. Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? Negligable Demographic and Health Surveys Program (2015) Mijikenda Mijikenda Ethnic Group Mijikenda/Swahili SCDO:1000134 A Cushitic speaking people comprising a small minority of Kenya's population. The Somali tend large herds of cattle, goats, sheep, and camels in the dry, arid lands of Northern Kenya. They are politically well organized and are united by both family allegiances and political treaties. The Somali also produce exquisitely carved headrests and woven artifacts. Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? Few but definitions not freely available Demographic and Health Surveys Program (2015) Somali Ethnic Group Somali SCDO:1000135 The Taita people are a Bantu tribe living in the Taita Hills on Kenya's southwest, near the Tanzania border and surrounding plains. Taita tribe actually consists of three separate but closely-related tribes: Wadawida (or Taita), Wasaghala (Sagalla) and Wataveta (Taveta). Perhaps change label to "Taveta"? Include the Wadawida (or Taita), Wasaghala (Sagalla) and Wataveta (Taveta) as sub-classes? Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? Negligable Demographic Health and Surveys Program (2015) Taita/Taveta Ethnic Group Taveta Ethnic Group Taita/Taveta SCDO:1000136 The Borana are a branch of the populous Oromo people found in southern Ethiopia and northern Kenya. Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? Negligable Demographic and Health Surveys Program (2015) Borana Ethnic Group Borana SCDO:1000137 It is the second largest sub-tribe of the Luhya ethnic group in Kenya. Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? None Demographic and Health Surveys Program (2015) Maragoli Ethnic Group Maragoli SCDO:1000138 The Pokot are a Kalenjin-speaking people whose language incorporates words from the neighboring Karamojong and Turkana. The Pokot live in an ecologically complex region that extends from the plains of eastern Uganda across the highlands of northwestern Kenya to the plains of Lake Baringo. Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? None Demographic Health and Surveys Program (2015) Pokot Ethnic Group Pokot SCDO:1000139 The Turkana tribe is a nomadic pastoralist people that inhabit the Turkana district in Kenya's Rift Valley Province. Turkana tribe is part of the Nilotic tribes and constitutes the second largest pastoralist community in Kenya after the Maasais. They speak the Turkana language, which is Nilotic and similar to the Maasai language. Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? None Demographic and Health Surveys Program (2015) Turkana Ethnic Group Turkana SCDO:1000141 Bassa is a Niger-Congo Kru language. Historians have traced the Bassa's origins back to Egypt nearly six thousand years ago. Due to their migration from Egypt to other parts of Africa, the Bassa in Liberia share a similar history with Bassa groups in other parts of the continent such as Nigeria (Bassa Nge), The Democratic Republic of the Congo (Bassaa la Mpasu), Togo (Basa'r), Senegal (Bassa-Ri), and Cameroon (Basaa Mpoo). Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? Negligable Demographic and Health Surveys Program (2013) Bassa Ethnic Group Bassa SCDO:1000142 Spectrophotometry involves the use of a spectrophotometer to measure the amount of light that a sample absorbs. The instrument operates by passing a beam of light through a sample and measuring the intensity of light reaching a detector. Sufficient SCDO:1000142 BAO:0000049 Spectrophotometry Method Spectrophotometry SCDO:1000143 A recommendation on the appropriate treatment and care of people with a specific disease or condition, based on the best available evidence, designed to help healthcare professionals in their work. Sufficient SCDO:1000143 SCDO (Jade Hotchkiss) FaBiO:d4e2515 Clinical Guideline Disease Management Guideline SCDO:1000144 Management protocols for the purposes of consistency and standardisation, which could also facilitate sharing of resources between centers for maximal utility. These recommendations have been developed for the South African setting, and it is intended to update them regularly to meet new demands and challenges. Probably not necessary to include in other ontologies. N A Alli, M Patel, H D Alli, et al. Recommendations for the management of sickle cell disease in South Africa. SAMJ. 2014, Vol. 104, No. 11. None South African Management Guidelines Recommendations for the Management of Sickle Cell Disease in South Africa SCDO:1000145 Guidelines for the management of specific clinical problems and protocols for various therapeutic procedures for patients with sickle cell disease and thalassaemia; to facilitate uniformity and standardization of care across different disciplines. Probably not necessary to include in other ontologies. National guideline for the control and management of sickle cell disease. 2014. None A Nigerian document. National Guideline for the Control and Management of Sickle Cell Disease SCDO:1000146 Guidelines for health care professionals for management of sickle cell disease in patients in the Tanzanian context. Probably not necessary to include in other ontologies. Management of Sickle Cell Disease - The United Republic of Tanzania None SCDO (Jade Hotchkiss) Tanzania Management Guidelines Management of Sickle Cell Disease - The United Republic of Tanzania SCDO:1000147 A booklet with information and standard guidelines to help parents learn about sickle cell disease and how to take care of their children with sickle cell disease. Probably not necessary to include in other ontologies. A parent's guide to managing sickle cell disease. Brent Sickle Cell and Thalassaemia Centre. 3rd Edition 2012. None A UK document.(for parents) A Parental Guide to Managing Sickle Cell Disease SCDO:1000148 A document that includes standards and guidelines for clinical care and recommendations for how care for adults with sickle cell disease should be delivered. Probably not necessary to include in other ontologies. Standards for Clinical Care of Adults with Sickle Cell Disease in the UK, 2nd Edition. 2018, Sickle Cell Society. None A UK document (for adults with SCD) Standards for Clinical Care of Adults with Sickle Cell Disease in the UK SCDO:1000149 The second edition of the Clinical Care Guidelines of the Sickle Cell Unit, containing revised and expanded guidelines for the management of sickle cell disease. It outlines a standard of care that is informed by best practice, taking into account resource limitations locally and regionally. It also contains patient information leaflets. Probably not necessary to include in other ontologies. Sickle Cell Disease: The Clinical Care Guidelines of the Sickle Cell Unit, 2015 None SCDO (Jade Hotchkiss) Jamaican Management Guidelines Sickle Cell Disease: The Clinical Care Guidelines of the Sickle Cell Unit SCDO:1000150 Standard of care guidelines that promote excellence in sickle cell care, and that lead to improved patient experiences around care and treatment. Probably not necessary to include in other ontologies. Segbefia C, Pendergrast J, Amid A, et al. 2015. Consensus Statement on the Care of Patients with Sickle Cell Disease in Canada. The Canadian Haemoglobinopathy Association. None A Canadian document. Consensus Statement on the Care of Patients with Sickle Cell Disease in Canada SCDO:1000151 A document that include standards and guidelines for clinical care and recommendations for how care for children with sickle cell disease should be delivered. Probably not necessary to include in other ontologies. Sickle cell disease in children, standards and guidelines for clinic care. 2nd edition. October 2010 None A UK document (for children with SCD) Sickle Cell Disease in Children, Standards and Guidelines for Clinic Care SCDO:1000152 Guidelines providing the best science-based recommendations to guide practice decisions for primary care providers and other clinicians, nurses, and staff who provide emergency or continuity care to individuals with sickle cell disease (SCD). They assist health care professionals in the management of common issues, including routine health maintenance, the recognition and treatment of common acute and chronic complications and comorbidities of SCD, as well as the indications for and monitoring of hydroxyurea and blood transfusion therapy. The guidelines address the care of infants, children, adolescents, and adults with SCD, with the goal of facilitating high-quality and appropriate care for all individuals with this disease. Probably not necessary to include in other ontologies. Evidence-Based Management of Sickle Cell Disease: Expert Panel Report, 2014 None USA Management Guidelines Children Evidence-Based Management of Sickle Cell Disease SCDO:1000153 A review of service delivery across Europe to children with sickle cell disease (SCD), reporting on the available minimum standards of care and future perspectives. Probably not necessary to include in other ontologies. None Colombatti R and Sainati L. Management of children with sickle cell disease in Europe: current situation and future perspectives. EMJ Hematol. 2016;4[1]:129-135. European document (Colombatti) Management of Children with Sickle Cell Disease in Europe: Current Situation and Future Perspectives SCDO:1000154 A document that describes various ways in which sickle cell disease can be managed and its complications can be prevented in children. Probably not necessary to include in other ontologies. None Am J Hematol. 2011 Jan;86(1):72-5. doi: 10.1002/ajh.21865. European document for children with SCD (Montalambert) ENERCA Clinical Recommendations for Disease Management and Prevention of Complications of Sickle Cell Disease in Children SCDO:1000155 Research conducted on members of families, examining the affects of genetics, the environment, or twin offspring. Sufficient SCDO:1000155 EDDA:familial_study Familial Studies Familial Study Family Based Study Family Study Family Study SCDO:1000157 The distinguishing qualities or prominent aspects of an individual person that have some relation with quality of life. Probably too specific to SCDO to be included in other ontologies? None SCDO (Jade Hotchkiss) Quality of Life Related Personal Attribute SCDO:1000158 Hemoglobin that has undergone conformational changes resulting in increased hydrophobicity that results in the formation of solid crystals consisting of hemoglobin particles. Request inclusion into the HPO, below "Abnormal Hemoglobin". None SCDO (Jade Hotchkiss) Crystallised Haemoglobin Crystallized Haemoglobin Crystallized Hemoglobin Haemoglobin Crystals Hemoglobin Crystals Crystallised Hemoglobin SCDO:1000159 When one beta-globin gene carries the hemoglobin S mutation (beta6Glu>Val) whereas the other carries a mutation that reduces the amount of beta-globin chain synthesised. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) Hemoglobin Genotype S/Beta Minus Thalassaemia SCDO:1000160 Work consisting of a set of statements, directions, or principles presenting current or future rules or policy. Guidelines may be developed by government agencies at any level, institutions, organizations such as professional societies or governing boards, or by the convening of expert panels. The text may be cursive or in outline form, but it is generally a comprehensive guide to problems and approaches in any discipline or activity. This concept relates to the general conduct and administration of health care activities rather than to specific decisions for a particular clinical condition. Do we rather want to use the more specific MESH term "Practice Guideline"? Sufficient SCDO:1000160 MESH:D016431 Guideline SCDO:1000161 A genotype whereby one HBB allele produces hemoglobin beta chains for normal adult hemoglobin and the other produces the abnormal hemoglobin beta chains of hemoglobin S. Individuals with this genotype are known to be carriers of the sickle cell trait. Request inclusion into relevant ontology None SCDO Haemoglobin Genotype AS Sickle Cell Trait Genotype Hemoglobin Genotype AS SCDO:1000162 The condition in which an individual with sickle cell trait shows symptoms of sickle cell disease such as anemia or acute chest syndrome. Clinical Sickle Cell Disease in the Heterozygous State Dominant Sickle Cell Disease Often these individuals have co-inherited another hemoglobin mutation that decreases hemoglobin solubility (eg, HbS-Antilles; Hb-Quebec-Chori; HbS-Oman; Hb Jamaica Plain). Other rare causes of symptomatic sickle cell trait include: mosaicism for cells in which only the sickle mutation was expressed due to post-zygotic uniparental disomy, and when sickle cell trait coexists with pyruvate kinase deficiency, which lowers the hemoglobin oxygen affinity, resulting in hemoglobin S polymerization and sickling. deprecated-Symptomatic Sickle Cell Trait true SCDO:1000163 A hemoglobinopathy in which the sickle mutation (HBB, Glu6Val) is inherited in combination with another beta-globin gene mutation, other thanHBB, Glu6Val. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) Compound Heterozygous Sickling Disorder Compound Heterozygous Sickle Cell Disease SCDO:1000164 Sickle cell disease caused by two mutations in the same beta globin allele, specifically the sickle cell mutation beta6 Glu > Val and a second beta68 Leu > Phe mutation.The other beta globin allele produces normal beta globin chains. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) Sickle Cell Disease A/Jamaica Plain SCDO:1000165 Sickle cell disease caused by two mutations in the same beta globin allele, specifically the sickle cell mutation (beta6 Glu > Val) and the hemoglobin O-Arab mutation (beta121 Glu > Lys). The other beta globin allele produces normal beta globin chains. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) Sickle Cell Disease A/S-Oman SCDO:1000166 Sickle cell disease caused by two mutations in the same beta globin allele, specifically the sickle cell mutation beta6 Glu > Val and a second beta 23 Val>Ile mutation. The other beta globin allele produces normal beta globin chains. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) Sickle Cell Disease C/S Antilles SCDO:1000170 A directive information entity that specifies how to establish a diagnosis based on clinical findings. Sufficient SCDO:1000170 AERO:0000001 Diagnosis Guideline SCDO:1000173 An ICD-10-CM code that can be used to indicate a diagnosis for reimbursement purposes as there are no codes with a greater level of specificity under each code. None SCDO (Jade Hotchkiss) Specific ICD-10-CM Code Billable ICD-10-CM Code SCDO:1000174 An ICD-10-CM diagnosis code that is not billable as there are more specific codes below it that contain a greater level of detail. None SCDO (Jade Hotchkiss) Non-specific ICD-10-CM Code Non-Billable ICD-10-CM Code SCDO:1000177 - Few but definitions not freely available ICD10CM:N48.32 N48.32 Priapism due to disease classified elsewhere N48.32 Priapism due to disease classified elsewhere SCDO:1000178 A data element in the SickleInAfrica Extended Demographics data capture instrument. None SCDO (Jade Hotchkiss) SickleInAfrica Extended Demographics DE SickleInAfrica Extended Demographics Data Element SCDO:1000179 A lack of production of hemoglobin E. Few but definitions not available SCDO (Jade Hotchkiss) Absent Haemoglobin E Haemoglobin E Absent Hemoglobin E Absent Normal Haemoglobin E Level Normal Hemoglobin E Level Absent Hemoglobin E SCDO:1000181 When the abnormal hemoglobin, hemoglobin E (HbE), has been detected in a blood sample. Few but definitions not available SCDO (Jade Hotchkiss) Haemoglobin E Present Haemoglobin E in Blood HbE Present HbE in Blood Hemoglobin E in Blood Hemoglobin E Present SCDO:1000187 When the level of hemoglobin A2 detected in a sample of blood falls in the normal range for HbA2. None SCDO (Jade Hotchkiss) Normal Haemoglobin A2 Level Normal HbA2 Level Normal Hemoglobin A2 Concentration Normal Hemoglobin A2 Level SCDO:1000197 A test to detect both HIV antibodies and HIV antigens (a part of the virus) in blood. Request inclusion into relevant ontology. None SCDO (Khuthala Mnika) Antibody/Antigen Tests It can take 2 to 6 weeks for a person’s body to make enough antigens and antibodies for a combination test to detect HIV infection. HIV Combination Test SCDO:1000198 A test to detect HIV in a person's blood. Request inclusion into relevant ontology. The more specific term "HIV-1 nucleic acid testing" is found in the OBI. None SCDO (Khuthala Mnika) NAT NATS can detect HIV infection about 7 to 28 days after a person has been infected with HIV. NATs are very expensive and not routinely used for HIV screening unless the person had a high-risk exposure or a possible exposure with early symptoms of HIV infection. HIV Nucleic Acid Test NAT SCDO:1000201 An abnormal albumin excretion rate of more than 300 mg/g urine creatinine. Request inclusion into relevant ontology Few but definitions not freely available Macro-albuminuria Macroalbuminuria High Level Albuminuria SCDO:1000205 A clinically severe form of sickle cell disease resulting when a person is homozygous for Hemoglobin C-Harlem. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) Hemoglobin C-Harlem Disease SCDO:1000206 Production of new arrangements of DNA by various mechanisms such as assortment and segregation, crossing over; gene conversion; genetic transformation; genetic conjugation; genetic transduction; or mixed infection of viruses. Sufficient SCDO:1000206 MESH:D011995 Recombination Recombination, Genetic Genetic Recombination SCDO:1000207 An exchange of DNA between matching or similar sequences. Sufficient SCDO:1000207 MESH:D059765 Homologous Recombinations Homologous Recombination SCDO:1000208 The reciprocal exchange of segments at corresponding positions along pairs of homologous chromosomes by symmetrical breakage and crosswise rejoining forming cross-over sites (Holliday junctions) that are resolved during chromosome segregation. Crossing-over typically occurs during meiosis but it may also occur in the absence of meiosis, for example, with bacterial chromosomes, organelle chromosomes, or somatic cell nuclear chromosomes. link this term to Sufficient SCDO:1000208 MESH:D003434 Crossing Over, Genetic Genetic Crossing Over SCDO:1000209 The homologous recombination event that occurs during meiosis and results in the delta beta globin fusion chains that replace hemoglobin subunit beta chains in the abnormal hemoglobin, Hemoglobin Lepore. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) Crossover between delta (HBD) and beta globin (HBB) gene loci SCDO:1000211 Clinical sickle cell disease in the heterozygous state due to an additional mutation on the same allele as the beta S mutation. Hemoglobin Jamaica Plain is an example of an abnormal hemoglobin structure caused by a double mutation in 1 Hb allele. None SCDO (Jade Hotchkiss) Dominant Sickle Cell Syndrome Dominant Sickle Syndrome Often these individuals have co-inherited another hemoglobin mutation that decreases hemoglobin solubility (eg, HbS-Antilles; Hb-Quebec-Chori; HbS-Oman; Hb Jamaica Plain). Other rare causes of symptomatic sickle cell trait include: mosaicism for cells in which only the sickle mutation was expressed due to post-zygotic uniparental disomy, and when sickle cell trait coexists with pyruvate kinase deficiency, which lowers the hemoglobin oxygen affinity, resulting in hemoglobin S polymerization and sickling. Dominant Sickle Cell Disease SCDO:1000212 deprecated Disease Caused by A/Jamaica Plain Genotype true SCDO:1000213 deprecated Disease Caused by A/S-Oman Genotype true SCDO:1000214 deprecated Disease Caused by C/S Antilles Genotype true SCDO:1000215 A hemoglobinopathy involving the presence of structurally abnormal hemoglobins and defects in the quantity of hemoglobins synthesised. Probably too specific to the SCDO to be included in other ontologies. None SCDO (Jade Hotchkiss) Structural and Quantitative Hemoglobinopathy SCDO:1000221 A genotype whereby one of the four alpha-globin genes is faulty, either as a result of a single nucleotide variant (SNP) or of a deletion. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) -/alpha alpha/alpha Alpha Thalassemia Silent Genotype SCDO:1000224 Increased susceptibility to bruising. Suggest update to label of HPO's "Bruising Susceptibility". "Bruising Susceptibility" and "Easy Bruisability" are not actually the same thing. Suggest update to label SCDO (Jade Hotchkiss) Bruisability, Bruising susceptibility, Easy bruising Bruise Easily Bruising Susceptibility Easy Bruising Easy Bruisability SCDO:1000225 A genotype whereby one HBB allele produces hemoglobin beta chains for normal adult hemoglobin and the other produces the abnormal hemoglobin beta chains for hemoglobin C. Individuals with this genotype are known to be carriers of the hemoglobin C trait. None SCDO (Clair Ingram) AC Genotype AC Hemoglobin Genotype Haemoglobin Genotype AC Hemoglobin C Trait Genotype beta / beta6Glu>Lys Hemoglobin Genotype AC SCDO:1000226 A genotype whereby one HBB allele produces hemoglobin beta chains for normal adult hemoglobin and the other produces the abnormal hemoglobin beta chains for hemoglobin D. Individuals with this genotype are known to be carriers of the hemoglobin D trait. None SCDO (Clair Ingram) AD Genotype AD Hemoglobin Genotype Haemoglobin Genotype AD Hemoglobin D Trait Genotype Hemoglobin Genotype AD SCDO:1000227 A genotype whereby one HBB allele produces hemoglobin beta chains for normal adult hemoglobin and the other produces the abnormal hemoglobin beta chains for hemoglobin E. Individuals with this genotype are known to be carriers of the hemoglobin E trait. Request inclusion into relevant ontology None SCDO (Clair Ingram) AE Genotype AE Hemoglobin Genotype Haemoglobin Genotype AE Hemoglobin E Trait Genotype beta / beta26Glu>Lys Hemoglobin Genotype AE SCDO:1000228 A genotype whereby one HBB allele produces hemoglobin beta chains for normal adult hemoglobin and the other produces the abnormal hemoglobin beta chains for hemoglobin O-Arab. Individuals with this genotype are known to be carriers of the hemoglobin O-Arab trait. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) AO-Arab Genotype AO-Arab Hemoglobin Genotype Haemoglobin Genotype AO-Arab beta / beta121Glu>Lys Hemoglobin Genotype AO-Arab SCDO:1000229 The homozygous genotype that involves a substitution of glutamic acid for a lysine at position 26 of beta-globin chains (hemoglobin E mutation) produced by both beta-globin gene (HBB) alleles. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) EE Genotype EE Hemoglobin Genotype Haemoglobin Genotype EE Hemoglobin E Genotype beta6Glu>Lys / beta26Glu>Lys Hemoglobin Genotype EE SCDO:1000230 The homozygous genotype that involves a hemoglobin D mutation in both beta-globin gene (HBB) alleles. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) DD Genotype DD Hemoglobin Genotype Haemoglobin Genotype DD Hemoglobin C Genotype Hemoglobin Genotype DD SCDO:1000231 The homozygous genotype that involves a substitution of glutamic acid for a lysine at position 121 of beta-globin chains (hemoglobin O-Arab mutation) produced by both beta-globin gene (HBB) alleles. Probably not necessary to include in other ontologies. None SCDO (Jade Hotchkiss) Haemoglobin Genotype O-Arab O-Arab Genotype O-Arab Hemoglobin Genotype beta121Glu>Lys / beta121Glu>Lys Hemoglobin Genotype O-Arab SCDO:1000232 The homozygous genotype that involves a substitution of glutamic acid for a lysine at position 6 of beta-globin chains (hemoglobin C mutation) produced by both beta-globin gene (HBB) alleles. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) CC Genotype CC Hemoglobin Genotype Haemoglobin Genotype CC Hemoglobin C Genotype beta6Glu>Lys / beta6Glu>Lys Hemoglobin Genotype CC SCDO:1000233 The presence of an amino acid substitution in either an alpha-, beta-, or gamma-globin chain such that its proximity to the heme iron in the hemoglobin molecule results in facilitated oxidation of the hemoglobin to yield excess methemoglobin. This can occur in either one or both alleles of the effected gene. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) Haemoglobin Genotype M Hemoglobin M Genotype Hemoglobin Genotype M SCDO:1000234 Hemoglobin M Disease is autosomal dominant, thus does not seem to have a "trait" condition. obsolete - Hemoglobin M trait Genotype true SCDO:1000235 Either homozygosity or heterozygosity for the HPFH1 mutation, a 106-KB deletion in the beta globin gene cluster. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) Hereditary Persistence of Fetal Hemoglobin Genotype SCDO:1000236 The homozygous genotype for Hemoglobin Lepore Boston that involves a crossover between both sets of delta (HBD) and beta globin (HBB) gene loci during meiosis. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) Hemoglobin Lepore Boston Genotype SCDO:1000237 The inheritance of one normal HBB gene along with an abnormal HBB gene that contains two amino acid substitutions, namely Glu6Val (HbS) and Asp73Asn. Request inclusion into NCIT below "Hemoglobin Trait". None SCDO (Jade Hotchkiss) Hb CH-Trait Erythrocytes from persons with Hb CH trait show some sickling in hypertonic saline without deoxygenation; this finding and the renal functional abnormalities are similar to those seen in persons with sickle cell trait and suggest that the renal concentrating defects in the two disorders have similar pathogeneses. Hemoglobin C-Harlem Trait SCDO:1000238 A mutation in the NADH-Cytochrome b5 Reductase 3 gene, CYB5R3, that contributes to the presence of methemoglobinemia (type I or II). Request inclusion into relevant ontology None DIA 1 Mutation Diaphorase Mutation Methemoglobinemia Mutation NADH-Cytochrome b5 Reductase 3 Mutation CYB5R3 Mutation SCDO:1000239 Deletion of one alpha-globin gene, either an HBA1 or HBA2 gene, which results in Alpha Thalassemia Silent (the person with the mutation is a silent carrier). Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) Heterozygous Deletion of HBA1 or HBA2 SCDO:1000240 Either a decrease in the proportion of hemoglobin A to below 96-98% of all hemoglobin, or a complete lack of hemoglobin A production. Probably too specific to be added to existing ontologies? None SCDO (Jade Hotchkiss) Reduced or Absent Hemoglobin A SCDO:1000241 A lack of production of normal adult hemoglobin. Request inclusion into HPO below "Abnormal Hemoglobin Concentration". Negligable SCDO (Jade Hotchkiss) Hemoglobin A Absent Absent Hemoglobin A SCDO:1000242 A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in individuals that are homozygotes (having two copies of the same mutant allele). Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) Autosomal Homozygous Recessive Inheritance Autosomal Recessive Homozygous SCDO:1000243 A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in individuals that are compound heterozygotes (whereby each copy of a gene has a distinct mutant allele). Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) Autosomal Recessive Compound Heterozygous Inheritance Autosomal Recessive Compound Heterozygous SCDO:1000244 A sickle cell disease phenotype in which an individual heterozygous for hemoglobin S also has a severe pyruvate kinase deficiency, which lowers the hemoglobin oxygen affinity, resulting in hemoglobin S polymerization and sickling. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) Sickle Cell Trait with a Severe Pyruvate Kinase Deficiency SCDO:1000247 A powder form of the optically active form of glutamine having L-configuration; to be administered orally. Suggest update to description in the Drug Ontology (DRON) for "Glutamine Oral Powder" (currently no description provided). Few but definitions not freely available SCDO (Jade Hotchkiss) Glutamine Oral Powder Glutamine Oral Powder Product Glutamine Powder L-Glutamine Powder Oral Glutamine Oral administration of L-glutamine oral powder is approved by the FDA to reduce the acute complications of sickle cell disease and sickle beta zero-thalassemia in adult and pediatric patients. L-Glutamine Oral Powder SCDO:1000250 A phenotype in which a specific molecular function is abnormal. Sufficient SCDO:1000250 FYPO:0000707 deprecated Abnormal Molecular Function true SCDO:1000251 An increase in red blood cell sensitivity to change in osmotic pressure. More specifically, the degree or proportion of hemolysis that occurs when a sample of red blood cells are subjected to osmotic stress by being placed in a hypotonic solution. What is normal osmotic fragility? Perhaps this can be included in the description. Suggest update to description in the HPO. Currently no description given. Include "Osmotic Fragility Test" in an appropriate location below "Diagnostics Tools" and link to this term. Suggest update to description. SCDO (Jade Hotchkiss) HP:0005502 Increased Erythrocyte Osmotic Fragility Increased Red Cell Fragility Increased Red Cell Osmotic Fragility SCDO:1000252 Is this not the same as "Increased Red Cell Osmotic Fragility"? See dc:source provided. What is normal osmotic resistance? Perhaps this can be included in the description. Suggest update to description in the HPO. Currently no description given. Include "Osmotic Fragility Test" in an appropriate location below "Diagnostics Tools" and link to this term. Few but definitions not freely available HP:0005546 Increased Red Cell Osmotic Resistance SCDO:1000253 A situation in which a specific biological process within an organism is abnormal. Include here "Intrahepatic Sinusoidal Sickling"? See paper "Liver involvement in sickle cell disease" by Emel GÜRKAN et al. Sufficient SCDO:1000253 FYPO:0005447 Abnormal Biological Process SCDO:1000254 When deoxygenated, malfunctioning or mutated hemoglobins clump together and form a long polymer. None SCDO (Jade Hotchkiss) Hemoglobin Polymerisation Polymerisation of Hemoglobin SCDO:1000255 Guidelines that examine current available evidence on indications for transfusion in sickle cell disease. Probably not necessary to include in other ontologies. Br J Haematol. 2017 Jan;176(2):192-209. doi: 10.1111/bjh.14383. Epub 2016 Nov 18. None Guidelines on Red Cell Transfusion in Sickle Cell Disease - Part II: Indications for Transfusion SCDO:1000256 This guideline addresses the management of an acute painful sickle cell episode in patients presenting to hospital until discharge. This includes the use of pharmacological and non-pharmacological interventions, identifying the signs and symptoms of acute complications, skills and settings for managing an acute painful episode, and the information and support needs of patients. Probably not necessary to include in other ontologies. None SCDO Sickle Cell Acute Painful Episode - Management of an Acute Painful Sickle Cell Episode in Hospital SCDO:1000257 A factsheet that shares steps to improve care in emergency departments (ED) of hospitals and clinics for people with sickle cell disease (SCD). It was created to help improve healthcare in the ED for patients with SCD. Probably not necessary to include in other ontologies. None Three Tips About Sickle Cell Disease Every Emergency Provider Needs to Know SCDO:1000258 A comprehensive guideline to aid physicians and other health care professionals in the management of patients with acute and chronic pain associated with sickle cell disease (SCD). The guideline covers the following information: an overview of the disease, the types and characteristics of pain associated with the disease, recommendations for pain assessment, methods for treatment of pain and a discussion of pain in the various developmental stages. It also includes discussions of pain assessment instruments. Probably not necessary to include in other ontologies. Am Fam Physician. 2000 Mar 1;61(5):1544-1550. None SCDO Practice Guidelines: Management of Pain in Sickle Cell Disease SCDO:1000259 A hemoglobin that shows characteristics of an abnormal hemoglobin, but its inheritance does not accompany any disability. Request inclusion into NCIT below "Hemoglobin"/"Hemoglobin Variant". None SCDO (Jade Hotchkiss) Unusual Hemoglobin Variant Unusual Hemoglobin SCDO:1000260 Any feeling of illness or physical or mental change that results from strenuous exercise. Suggest update to description in OMIM (currently no description provided). Few but definitions not freely available OMIM:MTHU024836 Symptom Induced by Strenuous Exercise SCDO:1000261 A condition due to a deficiency of one or more essential vitamins. (Dorland, 27th ed) Sufficient SCDO:1000261 MESH:D001361 Vitamin Deficiencies Vitamin Deficiency Avitaminosis SCDO:1000268 Abnormality originating in one or more muscles of the set of muscles in the body. Suggest update to description HP:0003011 Abnormality of the Musculature SCDO:1000276 An abnormal level of hemoglobin that occurs in one or more forms of Sickle Cell Disease (SCD). Probably too specific to SCD be included in other ontologies. None SCDO (Jade Hotchkiss) Abnormal Hemoglobin Level in SCD SCDO:1000280 Hemochromatosis that results from repeated blood transfusions. Request inclusion into relevant ontology None SCDO Transfusion Haemochromatosis Transfusion-Induced Iron Overload Transfusion Hemochromatosis SCDO:1000281 An acquired metabolic disorder characterized by iron accumulation in the tissues. Suggest inclusion into existing ontology. Few but definitions not freely available SCDO (Jade Hotchkiss) Secondary Hemochromatosis SCDO:1000289 When the abnormal hemoglobin, hemoglobin D-Punjab (Hb D-Punjab), has been detected in a blood sample. None SCDO (Jade Hotchkiss) Haemoglobin D-Punjab Present Haemoglobin D-Punjab in Blood Hb D-Punjab Present Hb D-Punjab in Blood Hemoglobin D-Punjab in Blood Hemoglobin D-Punjab Present SCDO:1000290 When the abnormal hemoglobin, hemoglobin G-Philadelphia (Hb G-Philadelphia), has been detected in a blood sample. None SCDO (Jade Hotchkiss) Haemoglobin G-Philadelphia Present Haemoglobin G-Philadelphia in Blood Hb G-Philadelphia Present Hb G-Philadelphia in Blood Hemoglobin G-Philadelphia in Blood Hemoglobin G-Philadelphia Present SCDO:1000291 When the abnormal hemoglobin, hemoglobin O-Arab (Hb O-Arab), has been detected in a blood sample. None SCDO (Jade Hotchkiss) Haemoglobin O-Arab Present Haemoglobin O-Arab in Blood Hb O-Arab Present Hb O-Arab in Blood Hemoglobin O-Arab in Blood Hemoglobin O-Arab Present SCDO:1000292 When the level of hemoglobin F detected in a sample of blood falls in the normal range for HbF. None SCDO (Jade Hotchkiss) Normal Haemoglobin F Level Normal HbF Level Normal Hemoglobin F Concentration Normal Hemoglobin F Level SCDO:1000295 The score obtained from a quality of life-related diagnostic instrument. Request inclusion into relevant ontology Negligable SCDO (Jade Hotchkiss) Quality of Life Score Quality of Life Assessment Score SCDO:1000296 The score obtained from the Adult Sickle Cell Quality-of-Life Measurement Information System (ASCQ-Me) diagnostic instrument. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) ASCQ-Me - Quality of Life in SCD Score Sickle Cell Disease Adult Quality of Life Questionnaire Assessment Score ASCQ-Me Score SCDO:1000297 A diagnostic instrument that involves an assessment of quality of life- and/or quality of care-related elements. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) Quality of Life and Care Diagnostic Instrument SCDO:1000298 A deteremination of the presence of hepatitis B virus surface antigen. Suggest update to label in NCIT (from "Hepatitis B Virus Surface Antigen Measurement") Suggest update to label NCIT:C64850 HBSAG Test HBsAg Test Hepatitis B Surface Antigen Test Hepatitis B Virus Surface Antigen Measurement If a person tests “positive,” then further testing is needed to determine if this is a new “acute” infection or a “chronic” hepatitis B infection. A positive HBsAg test result means that you are infected and can spread the hepatitis B virus to others through your blood. Hepatitis B Virus Surface Antigen Test SCDO:1000299 The determination of the surface antibody reaction of a sample to the Hepatitis B virus. Suggest update to label in NCIT (from "Hepatitis B Surface Antibody Measurement") Suggest update to label NCIT:C74711 HBSAB Test HBsAb Test Hepatitis B Virus Surface Antibody Test anti-HBs Test Hepatitis B Surface Antibody Test SCDO:1000300 The determination of the amount of Hepatitis B virus core antibody present in a sample. Suggest update to label in nCIT (from "Hepatitis B Virus Core Antibody Measurement") Suggest update to label NCIT:C96660 Anti-HBc Test HBCAB Test HBcAB Test Hepatitis B Virus Core Antibody Test A "positive" or "reactive" anti-HBc (or HBcAb) test result indicates a past or current hepatitis B infection. The core antibody does not provide any protection against the hepatitis B virus (unlike the surface antibod). This test can only be fully understood by knowing the results of the HBsAg and anti-HBs tests. A positive anti-HBc (or HBcAb) test result requires talking to your health care provider for a complete explanation of your hepatitis B status. Hepatitis B Core Antibody Test SCDO:1000301 A set of three blood tests (Hepatitis B Core Antibody Test, Hepatitis B Surface Antibody Test, and Hepatitis B Virus Surface Antigen Test) needed to fully understand whether a person is infected with Hepatitis B or not. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) Hepatitis B Panel Hepatitis B Panel of Blood Tests Hepatitis B Blood Panel SCDO:1000302 The determination of the amount of hepatitis B virus antibody present in a sample. Suggest update to label in NCIT (from "Hepatitis B Virus Antibody Measurement") Suggest update to label NCIT:C125944 HBAB Test Hepatitis B Antibody Test Hepatitis B Virus Antibody Test SCDO:1000303 The determination of the amount of hepatitis B virus core IgG antibody in a biological specimen. Suggest update to label in NCIT (from "Hepatitis B Virus Core IgG Antibody Measurement") Suggest update to label NCIT:C119280 HBCIGGAB Test Hepatitis B Virus Core IgG Antibody Test Hepatitis B Core IgG Antibody Test SCDO:1000304 The determination of the amount of Hepatitis B virus core IgM antibody present in a sample. Suggest update to label in NCIT (from "Hepatitis B Virus Core IgM Antibody Measurement") Suggest update to label NCIT:C96661 HBCIGMAB Test Hepatitis B Virus Core IgM Antibody Test Hepatitis B Core IgM Antibody Test SCDO:1000305 Exercise testing for evaluation of hypoxemia and/or desaturation that occurs on exertion. Suggest inclusion of term below "Pulse Oximetry" in the CMO. PhenX protocol: Pulse Oximetry (Exercise) #91001 Sufficient SCDO:1000305 phenX:91001 Pulse Oximetry (Exercise) SCDO:1000306 The determination of the amount of hepatitis C virus antigen present in a sample. Suggest update to label in NCIT (from "Hepatitis C Virus Antigen Measurement" Suggest update to label NCIT:C116196 HCAG Test Hepatitis C Virus Antigen Measurement Hepatitis C Virus Antigen Test SCDO:1000307 A determination of the presence of the hepatitis C virus antibody in a biological specimen. Suggest update to label and description in NCIT (from "Hepatitis C Antibody Measurement") Suggest update to label and description NCIT:C92535 HCAB Test Hepatitis C Antibody Measurement Hepatitis C Virus Antibody Test Hepatitis C Antibody Test SCDO:1000308 The determination of the amount of hepatitis C virus core antigen in a biological sample. Suggest update to label in NCIT (from "Hepatitis C Virus Core Antigen Measurement") Suggest update to label NCIT:C135424 HCCAG Test HCV Core Antigen Measurement HCV Core Antigen Test Hepatitis C Core Antigen Test Hepatitis C Virus Core Antigen Measurement Hepatitis C Virus Core Antigen Test SCDO:1000309 The determination of the surface antibody reaction of a sample to the Hepatitis C virus. Suggest update to label in NCIT (from "Hepatitis C Surface Antibody Measurement") Suggest update to label NCIT:C74712 Hepatitis C Surface Antibody Measurement Hepatitis C Surface Antibody Test SCDO:1000310 The determination of the amount of cystatin C present in a sample. Suggest update to label in NCIT (from "Cystatin C Measurement") Suggest update to label NCIT:C92290 CYSTATC Blood Test Cystatin C Blood Test SCDO:1000313 The visual output that a specific diagnostic device produces. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) Visual Output of a Diagnostic Device Diagnostic Device Visual Output SCDO:1000314 A bioassay to measure levels of red blood cell microparticles. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) Red Blood Cell Microparticles Assay SCDO:1000315 A quantitative measurement of the amount of HDL cholesterol present in a sample of serum. Suggest update to label in NCIT (from "Serum HDL Cholesterol Measurement") Suggest update to label NCIT:C61041 Serum HDL Cholesterol Measurement Serum HDL Cholesterol Test SCDO:1000316 A technique used to measure velocity and amount of blood flow and circulation in the living system. None SCDO (Jade Hotchkiss) Blood Flow Test SCDO:1000317 Any value resulting from the quantification of a morphological or physiological parameter pertaining to the heart. Suggest this description for this term in the CMO (it was recently described separately from another similar term" but's it's definition has not yet been ascribed). Suggest update to description CMO:0000670 Heart Measurement SCDO:1000318 An information entity, used in the diagnosis of medical conditions, that is a recording of the output of a diagnostic instrument. Request inclusion into relevant ontology Add terms/Variables obtained from: History of Head Trauma Diagnostic Instrument None SCDO (Jade Hotchkiss) Diagnostic Instrument Outcome Diagnostic Instrument Measurement SCDO:1000319 Questions asking the respondent about smoking status in his or her entire life. Request inclusion into relevant ontology None Cigarette Smoking Status Diagnostic Instrument SCDO:1000320 Questions asking an adult respondent about smoking status in his or her entire life. Request inclusion into relevant ontology PhenX protocol: Cigarette Smoking Status - Adult #30604 None SCDO (Jade hotchkiss) Cigarette Smoking Status Diagnostic Instrument - Adult SCDO:1000321 Questions asking an adolescentt respondent about smoking status in his or her entire life. Request inclusion into relevant ontology PhenX protocol: Cigarette Smoking Status - Adolescent #30603 None SCDO (Jade hotchkiss) Cigarette Smoking Status Diagnostic Instrument - Adolescent SCDO:1000322 A person who has never smoked a cigarette, not even one or two puffs. Other ontologies define this as "A person who was not smoking at the time of the interview and has smoked less than 100 cigarettes in their life." Not relevant to context of sickle cell SCDO (Jade Hotchkiss) Never Smoker SCDO:1000323 A person who was smoking on a daily basis at the time of the interview. Other ontologies define this as "Indicates a person who has smoked at least 100 cigarettes in his or her lifetime and who currently smokes every day." Not relevant to context of sickle cell SCDO (Jade Hotchkiss) Current Every-Day Smoker SCDO:1000324 A person who had smoked a cigarette in the past, and was smoking on some days, but not daily, at the time of the interview. Other ontologies define this as "Indicates a person who has smoked at least 100 cigarettes in his or her lifetime, who smokes now, but does not smoke every day." Not relevant to context of sickle cell SCDO (Jade Hotchkiss) Current Some-Day Smoker SCDO:1000325 A person who was not smoking at the time of the interview but has smoked a cigarette in the past, even if just one or two puffs Other ontologies define this as "A person who was not smoking at the time of the interview but has smoked at least 100 cigarettes in their life." Not relevant to context of sickle cell SCDO (Jade Hotchkiss) Former Smoker SCDO:1000326 A person who has smoked a cigarette in the past, even if just one or two puffs, but was unable to or refused to answer when asked when the last time was that they smoked a cigarette, even one or two puffs. None SCDO (Jade Hotchkiss) Ever-Smoker SCDO:1000327 A person who had smoked in the past 30 days at the time of the interview, but who had not smoked every day of the past 30 days. None SCDO (Jade Hotchkiss) Past 30-Day Smoker SCDO:1000328 A person who had smoked every day of the past 30 days at the time of the interview. None SCDO (Jade Hotchkiss) Past 30-Day Every-Day Smoker SCDO:1000329 Question asking the respondent if s/he has ever consumed any alcoholic beverage during his or her entire life. Suggest update to label in PhenX PhenX protocol: #30101 Suggest update to label phenX:030100 Alcohol - Lifetime Use Diagnostic Instrument SCDO:1000330 A nine-item, interviewer-administered questionnaire to screen for the presence of epilepsy in adults. Request inclusion into "PhenX Phenotypic Terms". This is in the PhenX toolkit but not in the ontology in BioPortal. It should probably be included there. None SCDO (Jade Hotchkiss) phenX:130401 Epilepsy Screener for Adults Epilepsy Screener - Adult SCDO:1000331 A nine-item, interviewer-administered questionnaire to screen for the presence of epilepsy in family members, including children and those who are deceased. Request inclusion into "PhenX Phenotypic Terms". This is in the PhenX toolkit but not in the ontology in BioPortal. It should probably be included there. None SCDO (Jade Hotchkiss) phenX:130402 Family History of Epilepsy Screening Interview Ottman Brief Epilepsy Screener - Proxy-reported Version Epilepsy Screener - Child/Proxy SCDO:1000332 A disruption to the efficacy of the executive functions, which is a group of cognitive processes that regulate, control, and manage other cognitive processes. Request inclusion into relevant ontology. Perhaps below "Behavioral Abnormality" in the HPO. Few but definitions not freely available Defects in Executive Function Executive Function Deficit Executive Dysfunction SCDO:1000333 A series of 21 age-specific questionnaires and scoring sheets designed to screen a child's skills in five developmental areas: fine motor, gross motor, problem solving, communication, and personal-social. A child's scores for each area are compared to cut-off scores to determine a need for monitoring or further assessment. Request inclusion into relevant ontology. Maybe below "Clinical or Research Assessment Questionnaire" in the NCIT. Global Mental Status Screener - Child #130702 Few but definitions not freely available The Ages & Stages Questionnaires, Third Edition (ASQ-3) Global Mental Status Screener - Child SCDO:1000336 The frequency of acute pain episodes due to sickle cell disease (SCD). Request inclusion into relevant ontology Add as sub-classes: (from protocol questions) - a term for the number of times an emergency room was visited because of a sickle cell painful event in the last 6 months - a term for the number of times the person was admitted to a hospital because of a sickle cell painful event in the last 12 months Not relevant to context of sickle cell. This term in PhenX currently refers to a diagnostic instrument. Frequency of Sickle Cell Pain Episodes SCDO:1000337 Questions from the National Epidemiologic Survey on Alcohol and Related Conditions-III (NESARC-III) related to their lifetime use of illicit and prescribed substances. Suggest update to label in PhenX PhenX protocol: Substances - Lifetime Use #31102 Suggest update to label Substances - Lifetime Use Diagnostic Instrument SCDO:1000338 A 26-item, self-administered scale completed by the parent that assesses the child's sleep behaviors in the past 6 months. The scale includes six subscales: disorders of initiating and maintaining sleep (items 1, 2, 3, 4, 5, 10, 11); sleep breathing disorders (items 13, 14, 15); disorders of arousal (items 17, 20, 21); sleep-wake transition disorders (items 6, 7, 8, 12, 18, 19); disorders of excessive somnolence (items 22, 23, 24, 25, 26); and sleep hyperhidrosis (score of the items 9, 16). Each item is rated on a 5-point, Likert-type scale (1 = Never; 5 = Always [daily]). Scores from individual items of each subscale are added together to give a subscale score, with higher scores indicating greater symptoms. Scores from the individual subscales can be added together to give a total score. Request inclusion into relevant ontology. Separate adult vs children instruments not shown in "PhenX Phenotypic Terms". PhenX protocol: Sleep Disorders Screener - Children #121002 None SCDO (Jade Hotchkiss) phenX:121002 Sleep Disturbances Scale for Children Sleep Disorders Screener - Children SCDO:1000339 A record of an individual's background in regard to head trauma. Request inclusion into relevant ontology. Perhaps as a sub-class of "History of Trauma" in "The Stroke Ontology"? PhenX uses this as their label for a questionnaire, but we're going to suggest they change that. Otherwise, don't see it in other ontologies. Not relevant to context of sickle cell SCDO (Jade Hotchkiss) History of Head Trauma SCDO:1000340 A record of an individual's history of stroke(s) and associated symptoms such as slurred speech, double vision, loss of vision, and paralysis. Request inclusion into NCIT below "Personal Medical History". Note: Is present in The Stroke Ontology. Few but definitions not freely available SCDO (Jade Hotchkiss) History of Stroke SCDO:1000341 A record of an individual's history of kidney failure. Request inclusion into NCIT as a sub-class of "Personal Medical History". PhenX uses this as their label for a questionnaire, but we're going to suggest they change that. Otherwise, don't see it in other ontologies. Not relevant to context of sickle cell SCDO (Jade Hotchkiss) History of Kidney Failure SCDO:1000342 A questionnaire to assess history of transfusion. Suggest update to label as we have done. We are using "History of Transfusion" below Personal Attribute. PhenX protocol: History of Transfusion #830201 Suggest update to label phenX:830200 History of Transfusion Diagnostic Instrument SCDO:1000343 A record of an individual's history of type 1 and type 2 diabetes. Request inclusion into NCIT as a sub-class of "Personal Medical History". PhenX uses this as their label for a questionnaire, but we're going to suggest they change that. Otherwise, don't see it in other ontologies. Not relevant to context of sickle cell SCDO (Jade Hotchkiss) History of Type 1 and Type 2 Diabetes SCDO:1000344 A questionnaire to assess males' pregnancy history. Suggest update to label and description in PhenX as we have done. We are using "Reproductive History" below Personal Attribute. PhenX protocol: Reproductive History - Male #101302 Suggest update to label and description. SCDO (Jade Hotchkiss) Reproductive History Diagnostic Instrument - Male SCDO:1000345 A questionnaire to assess females' pregnancy history. Suggest update to label and description in PhenX as we have done. We are using "Reproductive History" below Personal Attribute. PhenX protocol: Reproductive History - Female #101301 Suggest update to label and description. SCDO (Jade Hotchkiss) Reproductive History Diagnostic Instrument - Female SCDO:1000348 A questionnaire to assess sleep disorders, a broad group of disorders that can be caused by endogenous disturbances in the sleep-wake or timing cycles (American Psychiatric Association, 2000). Sufficient SCDO:1000348 phenX:121000 Sleep Disorders Screener SCDO:1000350 A test to assess the structure and function of the heart valves. Suggest update to label in PhenX (from "Heart Valve Function") PhenX protocol: Heart Valve Function #40501 Suggest update to label phenX:40501 Heart Valve Function Test SCDO:1000352 Measurement of the breathing capacity of an adult's lung by means of a spirometer. Suggest update to description in PhenX (currently the same for both adult and child protocols) PhenX protocol: Spirometry - Adult #91601 Suggest update to description SCDO (Jade Hotchkiss) Spirometry - Adult SCDO:1000353 Measurement of the breathing capacity of a child's lung by means of a spirometer. Suggest update to description in PhenX (currently the same for both adult and child protocols) PhenX protocol: Spirometry - Child #91602 Suggest update to description SCDO (Jade Hotchkiss) Spirometry - Child SCDO:1000354 Pattern of behavior which predisposes certain individuals to increased risk for contracting disease or sustaining personal injury. These behaviors may cluster into a risky lifestyle. Sufficient SCDO:1000354 MESH:D000073599 Health Risk Behaviors Risky Health Behavior Risky Health Behaviors Health Risk Behavior SCDO:1000355 Physical surroundings or conditions of a hospital or other health facility and influence of these factors on patients and staff. Sufficient SCDO:1000355 MESH:D006272 Health Facility Environment SCDO:1000356 Height above sea level or above the earth's surface. Sufficient SCDO:1000356 CSP:1035-6505 Altitude SCDO:1000357 A measure of educational progress reported using a questionnaire based approach, often used as a proxy for cognitive performance as the two are correlated. PhenX protocol: Current Educational Attainment #11001 Sufficient SCDO:1000357 EFO:0004784 Self Reported Educational Attainment SCDO:1000360 A gene that encodes one of the globin family proteins, which are globular heme-containing proteins and include androglobin, cryoglobin, hemoglobin subunits, myoglobin and neuroglobin. Suggest update to description in NCIT. Suggest update to description NCIT:C142196 Globin Gene Family Globin Genes Globin Gene SCDO:1000361 A gene that provides instructions for making a protein called alpha-globin. Request inclusion into relevant ontology Negligable SCDO (Jade Hotchkiss) Alpha-Globin Gene SCDO:1000362 A gene located in the beta-globin locus (or gene cluster) on chromosome 11. Include sub-classes?: HBE1 (encodes hemoglobin subunit epsilon) HBG1 HBG2 HBM HBQ1 HBZ Should this perhaps rather be something like "Beta-Globin Locus Gene"? To prevent confusion with the HBB Gene. Request inclusion into relevant ontology. Negligable SCDO (Jade Hotchkiss) Beta-Globin Gene SCDO:1000363 A member of the alpha-globin family. In humans, it is encoded in the alpha-globin gene cluster or locus, located on chromosome 16. Two hemoglobin subunit zeta chains combine with two hemoglobin subunit epsilon chains to form the embryonic Hemoglobin Gower 1. Sufficient SCDO:1000363 MESH:D055543 HBAZ Haemoglobin Subunit Zeta Haemoglobin Zeta Chain Hemoglobin Zeta Chain Zeta Globin Zeta-Globin Hemoglobin Subunit Zeta SCDO:1000364 An adult hemoglobin component normally present in hemolysates from human erythrocytes in concentrations of about 3%. The hemoglobin is composed of two alpha chains and two delta chains. The percentage of HbA2 varies in some hematologic disorders, but is about double in beta-thalassemia. Request inclusion into NCIT below "Hemoglobin"/"Normal Hemoglobin". Sufficient SCDO:1000364 MESH:D006443 A2, Hemoglobin HbA2 Normal Variant of Hemoglobin A alpha2delta2 Hemoglobin A2 SCDO:1000366 A mutation that contributes to decreased or absent synthesis of the delta- and beta-globin chains with a compensatory increase in expression of fetal gamma-chain synthesis. Request inclusion into relevant ontology None SCDO (Jade Hotchkiss) Delta Beta Thalassaemia Mutation Delta Beta Thalassemia Mutation SCDO:1000371 A health abnormality in a woman during pregnancy. Suggest update to description in HP. Currently no description. Suggest update to description SCDO (Jade Hotchkiss) HP:0002686 Maternal Health Problem Prenatal Maternal Abnormality SCDO:1000376 In situ death of bone within the humeral head due to disruption of blood supply. Request inclusion into NCIT as sub-class of "Avascular Necrosis of Humerus". None SCDO (Jade Hotchkiss) Aseptic Necrosis of the Humeral Head Avascular Necrosis of the Humeral Head Osteonecrosis of the Humeral Head SCDO:1000379 Health care services that are respectful of and responsive to the health beliefs, practices and cultural and linguistic needs of diverse patients. The provider and the patient each bring their individual learned patterns of language and culture to the health care experience which must be transcended to achieve equal access and quality health care. Sufficient SCDO:1000379 MESH:D065246 Care, Culturally Congruent Culturally Congruent Care Culturally Competent Care SCDO:1000383 Any kidney disorder occurring as a consequence of injury to the kidney. Few but definitions not available SCDO (Jade Hotchkiss) Kidney Complication Renal Complication SCDO:1000392 Promoter-specific RNA polymerase II transcription factor that binds to the GC box, one of the upstream promoter elements, in mammalian cells. The binding of Sp1 is necessary for the initiation of transcription in the promoters of a variety of cellular and viral GENES. Sufficient SCDO:1000392 MESH:D016329 Transcription Factor, Sp1 Sp1 Transcription Factor SCDO:1000394 A gene component is a component of a gene. Sufficient SCDO:1000394 SIO:010444 Gene Component SCDO:1000395 A gene regulatory component is a gene component that exerts a regulatory function. Sufficient SCDO:1000395 SIO:010085 Gene Regulatory Component SCDO:1000396 A gene enhancer is a short region of DNA that can be bound with proteins to enhance transcription levels of genes in a gene cluster. Sufficient SCDO:1000396 SIO:010086 Gene Enhancer SCDO:1000397 A gene promoter is a region of DNA that initiates transcription of a particular gene. Sufficient SCDO:1000397 SIO:010446 Gene Promoter SCDO:1000398 None Erythroid Specific Enhancer of Bcl11A BCL11A Erythroid Enhancer SCDO:1000401 A characteristic that further describes the nature of data. None SCDO (Jade Hotchkiss) Data Descriptor SCDO:1000402 The predominant publication type for articles and other items indexed for NLM databases. Sufficient SCDO:1000402 MESH:D016428 Journal Article SCDO:1000406 A characteristic or directive that further describes the nature of data sharing. None SCDO (Jade Hotchkiss) Data Sharing Descriptor SCDO:1000408 Requirements indicate additional conditions set for use of data. Suggest update to description in DUO Suggest update to description DUO:0000017 Data Use Requirements SCDO:1000421 The standard method of providing feedback to study participants regarding their information (data, biological samples, genetic material) that has been shared. None SCDO (Jade Hotchkiss) Policy for Feedback to Participant Policy for Returning Results Policy for Returning Results to Participant Participant Feedback Policy SCDO:1000422 An element or information entity that is required to be provided in consent forms. None SCDO (Jade Hotchkiss) Basic Element of a Consent Form SCDO:1000423 The policy regarding participants' right to withdraw their participation in a study. None SCDO (Jade Hotchkiss) Participant Withdrawal Policy SCDO:1000424 A course or principle of action adopted or proposed by a study. None SCDO (Jade Hotchkiss) Study Policy SCDO:1000425 A statement of what the key investigational purpose of the study is. None SCDO (Jade Hotchkiss) Study Focus Statement SCDO:1000426 A statement about how the researcher is obligated by law to report if the participant is found to have a communicable disease. None SCDO (Jade Hotchkiss) Communicable Disease - Report by Law Statement SCDO:1000429 The principles of professional conduct concerning the rights and duties of the physician, relations with patients and fellow practitioners, as well as actions of the physician in patient care and interpersonal relations with patient families. Sufficient SCDO:1000429 MESH:D004992 Medical Ethics SCDO:1000430 Concepts related to ethics, excluding types of ethics. None SCDO (Jade Hotchkiss) Ethics Related Concept SCDO:1000431 A protein expressed in enterocytes of the small intestine and released into the systemic circulation when there is intestinal damage. This protein plays a role in binding to saturated long-chain fatty acids with a high affinity and to unsaturated long-chain fatty acids with less affinity. Suggest update to description in NCIT Few but definitions not specific enough NCIT:C29616 FABPI Fatty Acid-Binding Protein, Intestinal I-FABP Intestinal-Type Fatty Acid-Binding Protein iFABP Intestinal Fatty-Acid Binding Protein SCDO:1000432 The level of intestinal fatty-acid binding protein in the systemic circulation (serum). Used to provide the evidence for intestinal injury due to VOC affecting the splanchnic vasculature. None SCDO (Jade Hotchkiss) Serum Intestinal Fatty-Acid Binding Protein Level Measured in ng/ml Serum iFABP Level SCDO:1000433 Damage inflicted on the intestine. Few but definitions not available SCDO (Jade Hotchkiss) Intestinal Damage Intestinal Injury SCDO:1000436 Adverse functional, metabolic, or structural changes in ischemic tissues resulting from the restoration of blood flow to the tissue (reperfusion), including swelling; hemorrhage; necrosis; and damage from free radicals. The most common instance is myocardial reperfusion injury. Sufficient SCDO:1000436 EFO:0002687 Hypoxia-Reoxygenation Injury Hypoxia/Reperfusion Injury IRI Ischaemia Reperfusion Injury Ischemia Reperfusion Injury Reoxygenation Injury Hypoxia-Reperfusion Injury SCDO:1000439 An increased circulating blood concentration of the intestinal fatty-acid binding protein. None SCDO (Jade Hotchkiss) Significantly high serum iFABP levels is evidence of intestinal injury. Elevated Serum iFABP Level SCDO:1000444 The level of L-selectin in the systemic circulation (serum). None SCDO (Jade Hotchkiss) Serum CD62L Level Soluble CD62L Serum L-Selectin Level SCDO:1000445 The number of aged neutrophils in a specified volume of blood, usually 1 cubic millimeter. None SCDO (Jade Hotchkiss) Activated Neutrophil Count Aged Neutrophil Count SCDO:1000448 A medication that is typically used for indications other than pain control but provides control of pain in some painful diseases. None Adjuvant Analgesic Agent Adjunct Analgesic Agent SCDO:1000449 An infusion of ketamine at a low dose (up to 5 µg/kg/min). None Low-dose ketamine infusion may be considered as an adjunct analgesic agent in patients with vaso-occlusive episodes who report continued severe pain despite high-dose opioid therapy, particularly those experiencing opioid-induced adverse effects. Low-Dose Ketamine Infusion SCDO:1000452 Pain that may be caused by or related to cellular, tissue, and systemic changes that occur during neoplasm growth, tissue invasion, and metastasis. Sufficient SCDO:1000452 MESH:D000072716 Cancer-Related Pain Pains, Neoplasm-Related Cancer Pain SCDO:1000455 The current age of a patient, calculated using the current date and the patient's date of birth and provided in years. None SCDO (Jade Hotchkiss) Calculated Current Age in Years Calculated Current Age (Years) SCDO:1000457 A type of consent that includes an aspect of timing (i.e. an indication of when consent was acquired). Request inclusion into ICO below "Informed Consent". None SCDO (Jade Hotchkiss) Temporal Consent Concept SCDO:1000458 Consent given prior to enrollment. Request inclusion into the Informed Consent Ontology. None SCDO (Jade Hotchkiss) Prospective Consent SCDO:1000459 Consent that is taken later after enrollment into study especially in emergency situations. Request inclusion into the Informed Consent Ontology. None SCDO (Victoria Nembaware) Deferred Consent SCDO:1000460 Informed consent given prior to enrollment. Request inclusion into ICO below "Informed Consent". None SCDO (Victoria Nembaware) Prospective Informed Consent SCDO:1000461 Consent obtained at a population level through public/community engagement where individual consenting is not feasible. This is normally done for low risk studies and/or in case of emergencies. Request inclusion into the Informed Consent Ontology. None SCDO (Victoria Nembaware) Waived Consent SCDO:1000462 A decision made by a research ethics committee. Request inclusion into the Informed Consent Ontology. None SCDO (Jade Hotchkiss) Research Ethics Committee Decision SCDO:1000463 When a research ethics committee approves a study's application for approval of their proposed research. Request inclusion into the Informed Consent Ontology. None SCDO (Jade Hotchkiss) Approval of Ethics SCDO:1000464 When a research ethics committee declines a study's application for approval of their proposed research. Request inclusion into the Informed Consent Ontology. None SCDO (Jade Hotchkiss) Disapproval of Ethics SCDO:1000465 A method in which a patient or their legal representative provides consent. Request inclusion into the Informed Consent Ontology. None SCDO (Jade Hotchkiss) Mode of Providing Consent SCDO:1000466 When the participant or a legal representative or family member provides consent by filling out and/or signing a written form. Request inclusion into the Informed Consent Ontology. None SCDO (Jade Hotchkiss) Written Consent SCDO:1000467 When the participant communicates consent orally rather than by filling out and signing a written form. Normally a witness is present when verbal consent is given. Request inclusion into the Informed Consent Ontology. None SCDO Verbal Consent SCDO:1000470 A unique identifier assigned to a study participant's data when it is registered in the SickleInAfrica data registry. None SCDO (Jade Hotchkiss) SickleInAfrica Participant Number SCDO:1000471 The name of the country where the sample or data was collected. Few but definitions not specific enough FLU:0000831 Country of Data Collection SCDO:1000472 The rules by which data are described and recorded. Not relevant to context of sickle cell SCDO (Jade Hotchkiss) Data Standards SCDO:1000474 A data element used to capture or facilitate the capture of data in a clinical or research assessment. None SCDO (Jade Hotchkiss) Clinical or Research Assessment Data Element SCDO:1000475 A type of question pertaining to a clinical or research assessment data element. None SCDO (Jade Hotchkiss) Clinical or Research Assessment Question Type SCDO:1000477 deprecated Field Type true SCDO:1000479 deprecated Calculation Field Type true SCDO:1000480 deprecated Checkbox Field Type true SCDO:1000481 deprecated Descriptive Field Type true SCDO:1000482 deprecated Dropdown Field Type true SCDO:1000483 deprecated Dropdown Multiple Choice Field Type true SCDO:1000484 deprecated Dropdown Single Choice Field Type true SCDO:1000485 deprecated File Upload Field Type true SCDO:1000486 deprecated Radio Field Type true SCDO:1000487 deprecated Text Box Field Type true SCDO:1000488 deprecated Notes Box Field Type true SCDO:1000489 deprecated Slider - Visual Analog Scale true SCDO:1000490 The situation, with regard to obtaining consent from a respondent, at a particular stage during a process. None SCDO (Jade Hotchkiss) Consent Status SCDO:1000492 A question that provides the respondent with specific answer options to choose from. None SCDO (Jade Hotchkiss) Close-Ended Question SCDO:1000493 A question that allows the respondent to give their own answer instead of selecting an answer from answer options. None SCDO (Jade Hotchkiss) Open-Ended Question SCDO:1000494 A close-ended question that provides two possible answers. None SCDO (Jade Hotchkiss) Dichotomous Question SCDO:1000495 A close-ended question that provides multiple answers for respondents to select from and allows for the selection of multiple options. None SCDO (Jade Hotchkiss) Multiple Choice Multiple Selection Question SCDO:1000496 A close-ended question that provides multiple answers for respondents to select from but allows for the selection of only one option. None SCDO (Jade Hotchkiss) Multiple Choice Single Selection Question SCDO:1000497 A dichotomous question that has answer options "true" and "false". None SCDO (Jade Hotchkiss) True-False Question SCDO:1000498 A dichotomous question that has answer options "yes" and "no". None SCDO (Jade Hotchkiss) Yes-No Question SCDO:1000501 A open ended question that restricts the nature of the text answer that can be provided by the respondent. None SCDO (Jade Hotchkiss) Open-Ended Question - Restricted SCDO:1000502 A open ended question that allows the respondent to respond in free text, without any restrictions on the nature of the text answer provided. None SCDO (Jade Hotchkiss) Open-Ended Question - Free Text SCDO:1000508 A data element in a SickleInAfrica data capture instrument. None SCDO (Jade Hotchkiss) SickleInAfrica DE SickleInAfrica Data Element SCDO:1000509 A data element in the SickleInAfrica core data capture instrument. None SCDO (Jade Hotchkiss) SickleInAfrica Core DE SickleInAfrica Core Data Element SCDO:1000510 The Sickle in Africa core data element that collects the concentration of albumin in the respondent's urine. Urinary albumin concentration urinary_microalbumin_conc Kidney Function Assay (Phenx protocols PX141401, PX141501 and PX141601 unless stated otherwise) µg/mL; PX141501 3 Number text SickleInAfrica CDE - Urinary Albumin Concentration Question SCDO:1000512 The Sickle in Africa core data element that records whether the respondent has consented as necessary. 1, Yes 2, No -7, Refused -9, Don't Know Has the patient consented? consent_obtained Consent 1 radio SickleInAfrica CDE - Informed Consent Obtained Question SCDO:1000513 An indication of whether informed consent was obtained from the respondent and/or their proxy. Few but definitions not available SCDO (Jade Hotchkiss) Informed Consent Obtained SCDO:1000514 Voluntary authorization given by a respondent and/or their proxy to be enrolled into a study as a research subject. Request inclusion into relevant ontology, perhaps the ICO. None SCDO (Jade Hotchkiss) Study Enrollment Consent SCDO:1000515 Voluntary authorization given by a study respondent and/or their proxy to have their specimen(s) stored. Request inclusion into relevant ontology, perhaps the ICO. None SCDO (Jade Hotchkiss) Specimen Storage Consent SCDO:1000516 Voluntary authorization given by a study paticipant to have their genetic material stored. Request inclusion into relevant ontology, perhaps the ICO. None SCDO (Jade Hotchkiss) Genetic Material Storage Consent 0 4 SCDO:1000520 The Sickle in Africa core data element that records the type(s) of informed consent obtained from the participant. 1, Study Enrollment Consent 2, Specimen Storage Consent 3, Genetic Material Storage Consent 4, Broad Consent Type(s) of informed consent obtained consent_type Consent 2 checkbox SickleInAfrica CDE - Type of Informed Consent Obtained Question SCDO:1000521 An indication of the type of informed consent that was obtained from the respondent and/or their proxies. None SCDO (Jade Hotchkiss) Type of Informed Consent Obtained SCDO:1000522 Time-related information that can be observed and is related to consent. None SCDO (Jade Hotchkiss) Temporal Observable of Consent SCDO:1000527 The current age of a patient, calculated using the current date and the patient's date of birth. None SCDO (Jade Hotchkiss) Calculated Current Age SCDO:1000532 The Sickle in Africa core data element that records the date on which the respondent signed the consent form for the relevant study. Date subject signed consent (dd/mm/yyyy) consent_date Consent 3 date_dmy text SickleInAfrica CDE - Date of Signing Consent Question SCDO:1000533 The Sickle in Africa core data element that records the name of the person who managed the process of consenting the respondent. Consented by: consented_by Consent 4 text SickleInAfrica CDE - Consented By Question SCDO:1000534 An indication of whether the respondent has had a blood transfusion since their last hospital visit. This is any transfusion before enrolment if it is the patient's first hospital visit. None SCDO (Jade Hotchkiss) Blood Transfusion Since Last Visit SCDO:1000535 An indication of whether the consent form used for obtaining informed consent from the respondent has been uploaded to the relevant electronic system. None SCDO (Jade Hotchkiss) Consent Form Uploaded SCDO:1000536 The name of the person who conducted consenting of the respondent. None SCDO (Jade Hotchkiss) Consented By SCDO:1000537 Time-related information that can be observed. Few but definitions not freely available SCDO (Jade Hotchkiss) Temporal Observable SCDO:1000538 Time-related information that can be observed and is related to a diagnosis. None SCDO (Jade Hotchkiss) Diagnosis Temporal Observable SCDO:1000539 The Sickle in Africa core data element that records the visit date, in the format dd/mm/yyyy. Visit date (dd/mm/yyyy) date_today Demographics 1 date_dmy text SickleInAfrica CDE - Visit Date Question SCDO:1000542 The Sickle in Africa core data element that records the site-specific unique identifier that was assigned to the study participant by the data collectors at the data collection site. Site participant number participant_number Demographics Site-specific ID eg. GH20181234 for Ghana, NG20184321 for Nigeria or TZ20180001 for Tanzania 3 text SickleInAfrica CDE - Site Participant Number Question SCDO:1000543 The Sickle in Africa core data element that records the respondent's date of birth in the format dd/mm/yyyy. Date of birth (dd/mm/yyyy) date_of_birth Demographics 9 date_dmy text SickleInAfrica CDE - Date of Birth Question SCDO:1000545 The current age of a patient, calculated using the current date and the patient's date of birth and provided in months. None SCDO (Jade Hotchkiss) Calculated Current Age in Months Calculated Current Age (Months) SCDO:1000546 The length of time that a person has lived since their birth up until the current day, as reported in years by the respondent. None SCDO (Jade Hotchkiss) Self-Reported Age in Years Self-Reported Current Age in Years Self-Reported Current Age (Years) SCDO:1000547 The Sickle in Africa core data element that records the respondent's age, as reported by the respondent in years. Self-reported age (in years) age_on_day_of_visit Demographics Age on day of visit 11 Number 0 125 RH text SickleInAfrica CDE - Self-Reported Age Question SCDO:1000548 The Sickle in Africa core data element that records the respondent's current marital status. 1, Married 2, Widowed 3, Divorced 4, Separated 5, Never been married/Annulled Current marital status marital_status Demographics 15 radio SickleInAfrica CDE - Current Marital Status Question SCDO:1000549 The Sickle in Africa core data element that records the date on which the respondent last received a blood transfusion. Date of blood transfusion transfusion_date Management Details 8 date_dmy [blood_transfusion] = "Yes" text SCDO (Jade Hotchkiss) SickleInAfrica CDE - Date of Transfusion Question SCDO:1000550 The Sickle in Africa core data element that records the type of SCD test that was used to diagnose the respondent, in the case where the type of test was not listed as an answer option in a previous data element. If other test, please specify: other_test SCD Diagnosis Details 6 [type_of_test] = '6' text SickleInAfrica CDE - SCD Other Test Question SCDO:1000551 The Sickle in Africa core data element that records the respondent's sex. 1, Male 2, Female 3, Intersex -7, Refused Respondent's sex respondent_sex Demographics 14 radio SickleInAfrica CDE - Sex Question SCDO:1000552 The Sickle in Africa core data element that records whether the respondent knows the date of their SCD diagnosis. 1, Yes 0, No Is date of SCD diagnosis known? diagnosis_date_known SCD Diagnosis Details 1 yesno SickleInAfrica CDE - Date of Diagnosis Known Question SCDO:1000553 Information or a description that further describes a diagnosis. None SCDO (Jade Hotchkiss) Diagnosis Descriptor SCDO:1000554 An indication of whether the date of the respondent's diagnosis of a disease is known by the respondent or the respondent's guardian. None SCDO (Jade Hotchkiss) Date of Diagnosis Known SCDO:1000555 An indication of whether the date of the respondent's SCD diagnosis is known by the respondent or the respondent's guardian. None SCDO (Jade Hotchkiss) Date of SCD Diagnosis Known SCDO:1000556 The Sickle in Africa core data element that records the respondent's date of diagnosis in the format dd/mm/yyyy. Date of SCD diagnosis (dd/mm/yyyy) exact_diagnosis_date SCD Diagnosis Details 2 date_dmy [diagnosis_date_known] = '1' text SickleInAfrica CDE - Date of Diagnosis Question SCDO:1000558 The date on which a diagnosis of sickle cell disease was made. None SCDO (Jade Hotchkiss) Date of SCD Diagnosis SCDO:1000566 The date on which a patient received a blood transfusion. None SCDO (Jade Hotchkiss) Date of Blood Transfusion SCDO:1000568 The year in which a sickle cell disease diagnosis was made. None SCDO (Jade Hotchkiss) Year of SCD Diagnosis SCDO:1000569 The month when a diagnosis was assigned to an individual's condition. None SCDO (Jade Hotchkiss) Month of Diagnosis SCDO:1000570 The month when a sickle cell disease diagnosis was made. None SCDO (Jade Hotchkiss) Month of SCD Diagnosis SCDO:1000571 The Sickle in Africa core data element that records the month of the year in which the respondent was diagnosed with SCD. -9, Don't know 1, 1 2, 2 3, 3 4, 4 5, 5 6, 6 7, 7 8, 8 9, 9 10, 10 11, 11 12, 12 Month of SCD diagnosis month_of_diagnosis SCD Diagnosis Details 4 [diagnosis_date_known] = '0' dropdown SickleInAfrica CDE - Month of Diagnosis Question SCDO:1000572 A diagnosis is the result of a medical investigation to identify a disorder from its signs and symptoms. Sufficient SCDO:1000572 SIO:001331 Diagnosis SCDO:1000573 The Sickle in Africa core data element that records the respondent's SCD test result. 1, SS 2, SBThal 3, SC 4, AS 5, Other SCD test result scd_test_result SCD Diagnosis Details SS = Sickle Cell Disease-SS | SBThal = Sickle Beta Thalassemia | SC = Sickle Cell Disease-SC | AS = Sickle Cell Trait 3 RH dropdown SickleInAfrica CDE - SCD Test Result Question SCDO:1000574 The result of a medical investigation to identify the type of sickle cell disease that a person has. None SCDO (Jade Hotchkiss) SCD Test Result SCDO:1000575 The Sickle in Africa core data element that records the type of SCD test that was used to diagnose the respondent. 1, HPLC 2, HBE 3, IEF 4, Basique 5, Acide 6, Sickle SCAN rapid test 7, Other Type of test? type_of_test SCD Diagnosis Details HPLC = High-Performance Liquid Chromatography| HBE = Hemoglobin Electrophoresis | IEF = Isoelectric Focusing| Basique = Basique SCD Test | Acide = Acide SCD Test 5 dropdown SickleInAfrica CDE - Type of SCD Test Question SCDO:1000576 A piece of information that further describes a diagnostic measurement. None SCDO (Jade Hotchkiss) Diagnostic Measurement Descriptor SCDO:1000577 The type of test that was used to obtain a sickle cell disease diagnosis. None SCDO (Jade Hotchkiss) Type of SCD Test SCDO:1000578 The Sickle in Africa core data element that records the respondent's SCD test result, in the case where the specific result was not listed as an answer option in a previous data element. If other SCD test result, please specify: other_scd_test_result SCD Diagnosis Details 4 text SickleInAfrica CDE - SCD Test Other Result Question SCDO:1000579 The Sickle in Africa core data element that records the respondent's ABO Blood Group. 1, A+ 2, A- 3, B+ 4, B- 5, O+ 6, O- 7, AB+ 8, AB- ABO blood group abo_blood_group SCD Diagnosis Details 7 dropdown SCDO (Jade Hotchkiss) SickleInAfrica CDE - Blood Group Question SCDO:1000580 A blood test that uses the principles of gel electrophoresis to separate out the various types of hemoglobin in order to determine the level of different types of hemoglobin in the blood. Placed as sub-class here according to position in the "Read Codes, Clinical Terms Version 3 (CTV3)" Ontology Few but definitions not available Electrophoresis - hemoglobin HBE Haemoglobin Electrophoresis Hb electrophoresis Hemoglobinopathy - electrophoresis Hgb electrophoresis Sickle cell - electrophoresis Thalassemia Screening Thallasemia - electrophoresis Hemoglobin Electrophoresis SCDO:1000582 A blood type containing type A red blood cell surface markers, with the presence of a protein called rhesus (Rh) factor. Few but definitions not available SCDO (Kambe Banda) A+ Blood group A Rh(D) positive Type A blood, Rh positive Blood Type A Positive SCDO:1000583 A blood type containing type A red blood cell surface markers, with the absence of a protein called rhesus (Rh) factor. SCDO (Kambe Banda) Few but definitions not available A- Blood group A Rh(D) negative Type A blood, Rh negative Blood Type A Negative SCDO:1000584 A blood type containing type B red blood cell surface markers, with the presence of a protein called rhesus (Rh) factor. Few but definitions not available SCDO (Kambe Banda) B+ Blood group B Rh(D) positive Type B blood, Rh positive Blood Type B Positive SCDO:1000585 A blood type containing type B red blood cell surface markers, with the absence of a protein called rhesus (Rh) factor. Few but definitions not available SCDO (Kambe Banda) B- Blood group B Rh(D) negative Type B blood, Rh negative Blood Type B Negative SCDO:1000586 A blood type containing no surface markers on red blood cells, with the presence of a protein called rhesus (Rh) factor. Few but definitions not available SCDO (Kambe Banda) Blood group O Rh(D) positive O+ Type O blood, Rh positive Blood Type O Positive SCDO:1000587 A blood type containing no surface markers on red blood cells, with the absence of a protein called rhesus (Rh) factor. Few but definitions not available SCDO (Kambe Banda) Blood group O Rh(D) negative O- Type O blood, Rh negative Blood Type O Negative SCDO:1000588 A blood type containing both type A and B red blood cell surface markers, with the presence of a protein called rhesus (Rh) factor. Few but definitions not available SCDO (Kambe Banda) AB+ Blood group AB Rh(D) positive Type AB blood, Rh positive Blood Type AB Positive SCDO:1000589 A blood type containing both type A and B red blood cell surface markers, with the absence of a protein called rhesus (Rh) factor Few but definitions not available SCDO (Kambe Banda) AB- Blood group AB Rh(D) negative Type AB blood, Rh negative Blood Type AB Negative SCDO:1000590 Information about how a patient's SCD is being managed. None SCDO (Jade Hotchkiss) SCD Management Details SCDO:1000591 The Sickle in Africa core data element that records the respondent's hydroxyurea use status (i.e. an indication of whether the respondent is using hydroxyurea). 1, Yes 0, No Using hydroxyurea using_hydroxyurea Management Details 1 RH yesno SickleInAfrica CDE - Hydroxyurea Use Question SCDO:1000592 An indication of whether the respondent is using hydroxyurea. None SCDO (Jade Hotchkiss) Hydroxyurea Use Status SCDO:1000593 The Sickle in Africa core data element that records the date on which the respondent started hydroxyurea therapy, in the format dd/mm/yyyy. Date of initiation of hydroxyurea therapy (dd/mm/yyyy) date_of_initiation_of_hydr Management Details 2 date_dmy text SickleInAfrica CDE - Hydroxyurea Initiation Date Question SCDO:1000594 The date on which hydroxyurea therapy was initiated. None SCDO (Jade Hotchkiss) Date of Hydroxyurea Therapy Initiation SCDO:1000595 The Sickle in Africa core data element that records whether the respondent is using penicillin V as a prophylaxis against bacterial infections. 1, Yes 2, No -6, NA Using penicillin V (prophylaxis) penicillin_v_prophylaxis Management Details 3 RH radio SickleInAfrica CDE - Penicillin V Use Question SCDO:1000596 An indication of whether the respondent is using penicillin V prophylaxis. None SCDO (Jade Hotchkiss) Penicillin V Prophylaxis Use Status SCDO:1000597 The Sickle in Africa core data element that records the respondent's folic acid use status (i.e. an indication of whether the respondent is using folic acid). 1, Yes 0, No Using folic acid folic_acid Management Details 5 RH yesno SickleInAfrica CDE - Folic Acid Use Question SCDO:1000598 An indication of whether the respondent is using folic acid. None SCDO (Jade Hotchkiss) Folic Acid Use Status SCDO:1000599 An indication of whether the respondent is using malaria prophylaxis. None SCDO (Jade Hotchkiss) Malaria Prophylaxis Status SCDO:1000600 The Sickle in Africa core data element that records whether the respondent is using malaria chemoprophylaxis (drugs that prevent malaria). 1, Yes 2, No -6, NA Using malaria chemoprophylaxis antimalaria_prophylaxis Management Details 4 radio SickleInAfrica CDE - Malaria Prophylaxis Question SCDO:1000601 The Sickle in Africa core data element that records whether the respondent's pneumococcal vaccination is up to date. 1, Yes 0, No Pneumococcal vaccination up to date pneumococcal_vacc_uptodate Management Details 6 RH yesno SickleInAfrica CDE - Pneumococcal Vaccination Question SCDO:1000602 An indication of whether the respondent is up to date with their pneumococcal vaccinations. None SCDO (Jade Hotchkiss) Pneumococcal Vaccination Status SCDO:1000604 The person who recorded the information about how a patient's condition is being managed. None SCDO (Jade Hotchkiss) Management Details Added By SCDO:1000605 Any assay which measures the amount, level or concentration of urea in whole blood. Sufficient SCDO:1000605 MMO:0000272 Blood Urea Analysis SCDO:1000606 The date on which the respondent's management details were added/recorded. None SCDO (Jade Hotchkiss) Management Details Add Date SCDO:1000607 The Sickle in Africa core data element that collects the red blood cell count in the respondent's blood, as measured by a complete blood count. Red blood cell count (RBC) cbc_redbloodcount Laboratory Results: Complete Blood Count (PhenX protocol PX220501 unless stated otherwise) million cells/µL 1 text SickleInAfrica CDE - Red Blood Cell Count Question SCDO:1000611 The Sickle in Africa core data element that collects the white blood cell count in the respondent's blood, as measured by a complete blood count. White blood cell count (WBC) cbc_whitebloodcount Laboratory Results: Complete Blood Count (PhenX protocol PX220501 unless stated otherwise) 1000 cells/µL 2 text SickleInAfrica CDE - White Blood Cell Count Question SCDO:1000612 Any structural abnormality of leukocytes (nucleated cells of the myeloid or lymphoid lineages, found in blood or other tissue). Suggest the HPO update their definition. Theirs currently is "An abnormality of leukocytes." Suggest update to description HP:0001881 Abnormal Leukocyte Morphology SCDO:1000615 The Sickle in Africa core data element that collects the platelet count in the respondent's blood, as measured by a complete blood count. Platelet count cbc_platelet_count Laboratory Results: Complete Blood Count (PhenX protocol PX220501 unless stated otherwise) 1000 cells/µL 3 text SickleInAfrica CDE - Platelet Count Question SCDO:1000619 The Sickle in Africa core data element that collects the concentration of hemoglobin in the respondent's blood, as measured by a complete blood count. Hemoglobin cbc_hemoglobin Laboratory Results: Complete Blood Count (PhenX protocol PX220501 unless stated otherwise) g/dL 4 text SickleInAfrica CDE - Hemoglobin - CBC Question SCDO:1000621 The Sickle in Africa core data element that collects the respondent's mean cell volume (MCV), as measured by a complete blood count. Mean cell volume (MCV) cbc_mean_cell_volume Laboratory Results: Complete Blood Count (PhenX protocol PX220501 unless stated otherwise) fL 5 text SickleInAfrica CDE - Mean Cell Volume Question SCDO:1000627 The Sickle in Africa core data element that collects the respondent's mean cell hemoglobin (MCH), as measured by a complete blood count. Mean cell hemoglobin (MCH) cbc_mean_cell_hemoglobin Laboratory Results: Complete Blood Count (PhenX protocol PX220501 unless stated otherwise) pg 6 text SickleInAfrica CDE - Mean Cell Hemoglobin Question SCDO:1000630 The Sickle in Africa core data element that collects the respondent's mean cell hemoglobin concentration (MCHC), as measured by a complete blood count. Mean cell hemoglobin concentration (MCHC) cbc_mchc Laboratory Results: Complete Blood Count (PhenX protocol PX220501 unless stated otherwise) g/dL 7 text SickleInAfrica CDE - Mean Cell Hemoglobin Concentration Question SCDO:1000637 The Sickle in Africa core data element that collects the respondent's red cell distribution width, as measured by a complete blood count. Red cell distribution width (RDW) cbc_redcelldistributionwidth Laboratory Results: Complete Blood Count (PhenX protocol PX220501 unless stated otherwise) % 8 text SickleInAfrica CDE - Red Cell Distribution Width Question SCDO:1000638 Red blood cell distribution width (RDW or RDW-CV or RCDW and RDW-SD) is a measure of the range of variation of red blood cell (RBC) volume that is reported as part of a standard complete blood count. Usually red blood cells are a standard size of about 6-8 μm in diameter. Certain disorders, however, cause a significant variation in cell size. Higher RDW values indicate greater variation in size. Normal reference range of RDW-CV in human red blood cells is 11.5-14.5%.[1] If anemia is observed, RDW test results are often used together with mean corpuscular volume (MCV) results to determine the possible causes of the anemia. It is mainly used to differentiate an anemia of mixed causes from an anemia of a single cause. Sufficient SCDO:1000638 EFO:0009188 RCDW RDW Red Cell Distribution Width Red Blood Cell Distribution Width SCDO:1000645 The Sickle in Africa core data element that collects the level of serum creatinine in the respondent's blood. Serum creatinine concentration serum_creatinine_conc Kidney Function Assay (Phenx protocols PX141401, PX141501 and PX141601 unless stated otherwise) mg/dL; PX141401 1 Number text SickleInAfrica CDE - Serum Creatinine Concentration Question SCDO:1000649 An abnormally increased amount of creatinine in the blood. Suggest update to description in HPO (include the word "abnormally") Suggest update to description HP:0003259 Elevated Creatinine High Blood Creatinine Level Increased Creatinine Increased Serum Creatinine Elevated Serum Creatinine SCDO:1000650 The Sickle in Africa core data element that collects the concentration of creatinine in the respondent's urine. Urinary creatinine concentration urinary_creatinine_conc Kidney Function Assay (Phenx protocols PX141401, PX141501 and PX141601 unless stated otherwise) mg/dL; PX141601 4 Number text SickleInAfrica CDE - Urinary Creatinine Concentration Question SCDO:1000657 The Sickle in Africa core data element that collects the level of alanine aminotransferase in the respondent's blood. Alanine aminotransferase level results_of_alanine_at_assay Liver Function Assay (PhenX protocol PX190801 unless stated otherwise) IU/L 1 Number text SCDO (Jade Hotchkiss) SickleInAfrica CDE - Alanine Aminotransferase Level Question SCDO:1000660 The Sickle in Africa core data element that collects the level of aspartate aminotransferase in the respondent's blood. Aspartate aminotransferase level results_of_aspartate_at_assay Liver Function Assay (PhenX protocol PX190801 unless stated otherwise) IU/L 2 Number text SCDO (Jade Hotchkiss) SickleInAfrica CDE - Aspartate Aminotransferase Level Question SCDO:1000662 The Sickle in Africa core data element that collects the level of alkaline phosphatase in the respondent's blood. Alkaline phosphatase level results_of_alkaline_phosphatase_assay Liver Function Assay (PhenX protocol PX190801 unless stated otherwise) IU/L 3 Number text SCDO (Jade Hotchkiss) SickleInAfrica CDE - Alkaline Phosphatase Level Question SCDO:1000663 A quantitative measurement of alkaline phosphatase present in a blood sample. Few but definitions not available SCDO (Jade Hotchkiss) Alkaline Phosphatase Test Alkaline Phosphatase Blood Test SCDO:1000669 A multiplexed qualitative point-of-care immunoassay used for the rapid diagnosis of sickle cell disorders. The test is made up of three indicators which detect the presence of hemoglobins A, S, and C, allowing the user to rapidly distinguish between normal, carrier, and sickle cell samples. None SCDO (Jade Hotchkiss) Sickle SCAN Rapid Test SCDO:1000673 An indication of a person's current status in terms of living with a person as though married (in a romantic relationship and living together but not married). None SCDO (Jade Hotchkiss) Current Partner Status SCDO:1000679 An indication of whether a person has previously lived with someone as though married (in a romantic relationship and lived together but were not married). None SCDO (Jade Hotchkiss) Past Partner Status SCDO:1000680 The Sickle in Africa core data element that collects the level of billirubin in the respondent's blood. Total billirubin concentration billirubin_total_billirubin_conc Laboratory Results: Bilirubin Level (PhenX protocol PX0810901 unless stated otherwise) mg/dL 1 Number text SickleInAfrica CDE - Total Bilirubin Concentration Question SCDO:1000682 The Sickle in Africa core data element that collects the level of lactate dehydrogenase in the respondent's blood. Lactate dehydrogenase level lactate_dehydrogenase_conc Laboratory Results: Lactate Dehydrogenase Level (PhenX protocol PX0811001 unless stated otherwise) IU/L 1 Number text SickleInAfrica CDE - Lactate Dehydrogenase Level Question SCDO:1000684 A decreased or reduced level of the enzyme lactate dehydrogenase in serum. The current label in HPO is "Reduced lactate dehydrogenase B level". Seems the "B" in the label and the comment that refers to the B subunit should be removed. Suggest update to label HP:0045041 Decreased Lactate Dehydrogenase Level Reduced Lactate Dehydrogenase Level SCDO:1000685 The Sickle in Africa core data element that collects the reticulocyte count in the respondent's blood, as measured by a complete blood count. Number of reticulocytes reticulocyte_amount Laboratory Results: Reticulocyte Count (PhenX protocol PX0810601 unless stated otherwise) 1000 cells/µL 1 Number text SickleInAfrica CDE - Reticulocyte Count Question SCDO:1000686 A test used to measure the reticulocyte count (number of reticulocytes in a given volume of blood). Few but definitions not available SCDO (Jade Hotchkiss) Retic Count Reticulocyte Count Test Reticulocyte Count Assay SCDO:1000687 The Sickle in Africa core data element that records the hemoglobins for which assay results were recorded. 1, Hb A 2, Hb F 3, Hb S 4, Hb C 5, Hb E 6, Hb A2 7, Hb D-Punjab 8, Hb G-Philadelphia 9, Hb O-Arab For which hemoglobins were assay results recorded? scd_hemoglobin_assay_results Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise) Select all relevant options 1 LH checkbox SickleInAfrica CDE - Hb Assay Results Recorded Question SCDO:1000688 The hemoglobins for which assay results were recorded. None SCDO (Jade Hotchkiss) Hemoglobin Assay Results Recorded SCDO:1000689 Hemoglobin G Philadelphia (HbG Phil) is a structural variant of the hemoglobin molecule that involves the alpha chain rather than the beta chain. It has a frequency of about 1 in 5,000 African Americans, but has been reported in other ethnic groups in the Mediterranean region as well, HbG Phil itself has no clinical consequences. The only finding of clinical interest is the mild microcytosis. While this molecule has no clinical consequences, the presence helps to distinguish HbG from HbD that shares its electrophoretic migration on HPLC and gel electrophoresis and which does have consequences when it occurs with sickle trait. Sufficient SCDO:1000689 LNC:LP16433-2 Hb G-Phil Hb G-Philadelphia HbG Phil Hemoglobin G Philadelphia Hemoglobin G-Philadelphia SCDO:1000690 The amount of hemoglobin A present in a specified volume of blood. Negligible SCDO (Jade Hotchkiss) Haemoglobin A Level Hemoglobin A Level SCDO:1000691 The Sickle in Africa core data element that collects the proportion of the respondent's hemoglobin that consists of hemoglobin A. Record the levels of Hb A if measured. hba2 Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise) % 2 Number [scd_hemoglobin_assay_results(1)] = '1' text SickleInAfrica CDE - Hemoglobin A Level Question SCDO:1000692 The amount of hemoglobin S present in a specified volume of blood. Few but definitions not available SCDO (Jade Hotchkiss) Haemoglobin S Level Hemoglobin S Level SCDO:1000693 The Sickle in Africa core data element that collects the proportion of the respondent's hemoglobin that consists of hemoglobin S. Record the levels of Hb S if measured. hbs Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise) % 4 Number [scd_hemoglobin_assay_results(3)] = '1' text SickleInAfrica CDE - Hemoglobin S Level Question SCDO:1000694 The Sickle in Africa core data element that collects the proportion of the respondent's hemoglobin that consists of hemoglobin C. Record the levels of Hb C if measured. hbc Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise) % 5 Number [scd_hemoglobin_assay_results(4)] = '1' text SickleInAfrica CDE - Hemoglobin C Level Question SCDO:1000695 The amount of hemoglobin C present in a specified volume of blood. Few but definitions not available SCDO (Jade Hotchkiss) Haemoglobin C Level Hemoglobin C Level SCDO:1000696 The Sickle in Africa core data element that collects the proportion of the respondent's hemoglobin that consists of hemoglobin E. Record the levels of Hb E if measured. hbe Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise) % 6 Number [scd_hemoglobin_assay_results(5)] = '1' text SickleInAfrica CDE - Hemoglobin E Level Question SCDO:1000697 The amount of hemoglobin E present in a specified volume of blood. Few but definitions not available SCDO (Jade Hotchkiss) Haemoglobin E Level Hemoglobin E Level SCDO:1000698 The amount of hemoglobin A2 present in a specified volume of blood. Few but definitions not available SCDO (Jade Hotchkiss) Haemoglobin A2 Level Hemoglobin A2 Level SCDO:1000699 The Sickle in Africa core data element that collects the proportion of the respondent's hemoglobin that consists of hemoglobin A2. Record the levels of Hb A2 if measured. hb_a2 Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise) % 7 Number [scd_hemoglobin_assay_results(6)] = '1' text SickleInAfrica CDE - Hemoglobin A2 Level Question SCDO:1000700 The Sickle in Africa core data element that collects the proportion of the respondent's hemoglobin that consists of hemoglobin D-Punjab. Record the levels of Hb D-Punjab if measured. hb_dpunjab Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise) % 8 Number [scd_hemoglobin_assay_results(7)] = '1' text SickleInAfrica CDE - Hemoglobin D-Punjab Level Question SCDO:1000701 The amount of hemoglobin D-Punjab present in a specified volume of blood. Few but definitions not available SCDO (Jade Hotchkiss) Haemoglobin D-Punjab Level Hemoglobin D-Punjab Level SCDO:1000702 The Sickle in Africa core data element that collects the proportion of the respondent's hemoglobin that consists of hemoglobin G-Philadelphia. Record the levels of Hb G-Philadelphia if measured. hb_gphilidelphia Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise) % 9 Number [scd_hemoglobin_assay_results(8)] = '1' text SickleInAfrica CDE - Hemoglobin G-Philadelphia Level Question SCDO:1000703 The amount of hemoglobin G-Philadelphia present in a specified volume of blood. None SCDO (Jade Hotchkiss) Haemoglobin G-Philadelphia Level Hemoglobin G-Philadelphia Level SCDO:1000704 The Sickle in Africa core data element that collects the proportion of the respondent's hemoglobin that consists of hemoglobin O-Arab. Record the levels of Hb O-Arab if measured. hb_o_arab Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise) % 10 Number [scd_hemoglobin_assay_results(9)] = '1' text SickleInAfrica CDE - Hemoglobin O-Arab Level Question SCDO:1000705 The amount of hemoglobin O-Arab present in a specified volume of blood. None SCDO (Jade Hotchkiss) Haemoglobin O-Arab Level Hemoglobin O-Arab Level SCDO:1000706 The Sickle in Africa core data element that collects the proportion of the respondent's hemoglobin that consists of hemoglobin F. Record the levels of Hb F if measured. hbf_percent Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise) % 3 Number [scd_hemoglobin_assay_results(2)] = '1' text SickleInAfrica CDE - Hemoglobin F Level Question SCDO:1000707 The amount of hemoglobin F present in a specified volume of blood. Few but definitions not available SCDO (Jade Hotchkiss) Haemoglobin F Level Hemoglobin F Level SCDO:1000708 The sex of the respondent's spouse, as provided by the respondent. None SCDO (Jade Hotchkiss) Sex of Spouse SCDO:1000709 The sex of the respondent's partner (where the partner is not a spouse), as provided by the respondent. None SCDO (Jade Hotchkiss) Sex of Partner SCDO:1000711 The Sickle in Africa core data element that collects the respondent's body temperature. Patient's body temperature body_temperature Vital Signs degrees Celsius 1 Number 13 46 text SCDO (Jade Hotchkiss) SickleInAfrica CDE - Body Temperature Question SCDO:1000714 The Sickle in Africa core data element that collects the respondent's respiratory rate. Patient's respiratory rate respiratory_rate Vital Signs breaths per minute 3 Number text SickleInAfrica CDE - Respiratory Rate Question SCDO:1000717 The Sickle in Africa core data element that collects the respondent's partial pressure of carbon dioxide in their arterial blood, as measured by an arterial blood gas test. Partial pressure of carbon dioxide (PaCO2) partial_pressure_co2 Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) mmHg 1 Number text SickleInAfrica CDE - Partial Pressure CO2 Question SCDO:1000722 The Sickle in Africa core data element that collects the respondent's partial pressure of oxygen their arterial blood, as measured by an arterial blood gas test. Partial pressure of oxygen (PaO2) partial_pressure_of_oxygen Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) mmHg 2 Number text SickleInAfrica CDE - Partial Pressure O2 Question SCDO:1000723 The pressure exerted by oxygen dissolved in the blood, indicating how well oxygen is able to move from the airspace of the lungs into the blood. Few but available definitions not adequate CMO:0000381 Oxygen Tension PaO2 Partial Pressure of Blood Oxygen Partial Pressure of Blood Oxygen (Po2) Partial Pressure of Oxygen (PaO2) Po2 Partial Pressure of Oxygen SCDO:1000724 The Sickle in Africa core data element that collects the respondent's arterial oxygen saturation (oxyhemoglobin saturation), as measured by an arterial blood gas test. Oxyhemoglobin saturation (HbO2) oxyhemoglobin_saturation Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) % 3 Number text SickleInAfrica CDE - Oxyhemoglobin Saturation Question SCDO:1000725 The Sickle in Africa core data element that collects the respondent's carboxyhemoglobin to total hemoglobin ratio, as measured by an arterial blood gas test. Carboxyhemoglobin (COHb) carboxyhemoglobin Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) % 4 Number text SCDO (Jade Hotchkiss) SickleInAfrica CDE - Carboxyhemoglobin Question SCDO:1000726 The Sickle in Africa core data element that collects the respondent's methemoglobin to total hemoglobin ratio, as measured by an arterial blood gas test. Methemoglobin (MetHb) methemoglobin Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) % 5 Number text SickleInAfrica CDE - Methemoglobin Question SCDO:1000727 The ratio of methemoglobin compared to total hemoglobin present in a sample. The measurement may be expressed as a ratio or percentage. Used term from existing ontology but will suggest they update their label and description to ours. EFO:0009226 HGBMHGB MetHb Saturation Methemoglobin Saturation Methemoglobin to Total Hemoglobin Ratio Measurement Methemoglobin/Total Hemoglobin Methemoglobin to Total Hemoglobin Ratio SCDO:1000728 The ratio of carboxyhemoglobin compared to total hemoglobin present in a sample. The measurement may be expressed as a ratio or percentage. Used term from existing ontology but will suggest they update their label and description to ours. EFO:0009203 COHb Saturation Carboxyhemoglobin Saturation Carboxyhemoglobin/Total Hemoglobin Carboxyhemoglobin to Total Hemoglobin Ratio SCDO:1000729 An elevated concentration in the blood of methemoglobin, which is the ferric (Fe(3+)) form of hemoglobin. Few but definitions not available SCDO (Jade Hotchkiss) Methemoglobin Increased Raised Methemoglobin Injury or toxic agents can convert a larger proportion of hemoglobin to methemoglobin, which does not function reversibly as an oxygen carrier and thus less oxygen is made available to the tissues. Increased Methemoglobin SCDO:1000730 A site-specific unique identifier assigned to a study participant by the data collectors at the data collection site. None SCDO (Jade Hotchkiss) Site Participant Number SCDO:1000731 A unique identifier provided on SCD passports. None SCDO (Jade Hotchkiss) SCD Passport Number SCDO:1000732 The Sickle in Africa core data element that records the unique identifier that was assigned to the study participant's data when it was registered in the SickleInAfrica data registry. SickleInAfrica Participant Number record_id text SickleInAfrica CDE - SickleInAfrica Participant Number SCDO:1000734 The Sickle in Africa core data element that calculates the respondent's age in months, using the visit date and birth date collected by other core data elements. Calculated age (in months) calc_age_on_day_of_visit Demographics datediff([date_today],[date_of_birth], "M","dmy") Age on day of visit 10 RH calc SCDO (Jade Hotchkiss) SickleInAfrica CDE - Age In Months Calculation SCDO:1000738 A data capture instrument designed and applied by the Sickle In Africa Consortium. None Consent Demographics SCD Diagnosis Details Management Details Laboratory Results: Complete Blood Count (PhenX protocol PX220501 unless stated otherwise) Kidney Function Assay (Phenx protocols PX141401, PX141501 and PX141601 unless stated otherwise) Liver Function Assay (PhenX protocol PX190801 unless stated otherwise) Laboratory Results: Bilirubin Level (PhenX protocol PX0810901 unless stated otherwise) Laboratory Results: Lactate Dehydrogenase Level (PhenX protocol PX0811001 unless stated otherwise) Laboratory Results: Reticulocyte Count (PhenX protocol PX0810601 unless stated otherwise) Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise) Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) SCDO (Jade Hotchkiss) SickleInAfrica Core Data Element Instrument SCDO:1000751 The Sickle in Africa core data element that collects the total concentration of hemoglobin in the respondent's blood. Total hemoglobin (Hbtotal) total_hemoglobin Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise) g/dL 11 Number text SickleInAfrica CDE - Total Hemoglobin Question SCDO:1000753 An assay to determine the body temperature of an evaluant using an oral thermometer. PhenX protocol: Body Temperature - Oral Thermometers #810102 None SCDO (Jade Hotchkiss) Oral Temperature Taking Body Temperature - Oral Measurement Assay SCDO:1000754 An assay to determine the body temperature of an evaluant using a tympanic (i.e. ear) thermometer. PhenX protocol: Body Temperature - Tympanic Thermometers #810101 None SCDO (Jade Hotchkiss) Tympanic Temperature Taking Body Temperature - Tympanic Measurement Assay SCDO:1000755 The temperature of the oral cavity. Sufficient SCDO:1000755 VSO:0000025 Oral Body Temperature Oral Temperature SCDO:1000756 The temperature of the external acoustic tube. Sufficient SCDO:1000756 VSO:0000045 Tympanic (ear) Temperature Tympanic Body Temperature Tympanic Temperature SCDO:1000757 The temperature of the lumen of the rectum. Sufficient SCDO:1000757 VSO:0000033 Rectal Body Temperature Rectal Temperature SCDO:1000758 The temperature of the axillary fossa. Sufficient SCDO:1000758 VSO:0000003 Armpit Temperature Axillary (armpit) Temperature Axillary Temperature SCDO:1000759 The Sickle in Africa core data element that records the type of body temperature that was taken for the respondent. 1, Oral Temperature 2, Tympanic (ear) Temperature 3, Axillary (armpit) Temperature 4, Rectal Temperature Type of body temperature taken type_of_temp Vital Signs 2 dropdown SickleInAfrica CDE - Type of Temperature Question SCDO:1000763 Type of Body Temperature SCDO:1000766 An answer to a question where the answer is a year between 1900 and the current year, selected from a provided list of years. None SCDO (Jade Hotchkiss) Year 1900 - Current SCDO:1000767 An answer to a question where the answer is a month between 1 - 12, selected form a list of months. None SCDO (Jade Hotchkiss) Month 1 - 12 SCDO:1000768 Waiting for description for this. Acide SCDO:1000769 Waiting for description for this. Basique SCDO:1000774 - Few but definitions not available ICD10CM:D57.03 D57.03 Hb-SS disease with cerebral vascular involvement Sickle cell anemia with cerebral vascular involvement D57.03 Hb-SS disease with cerebral vascular involvement SCDO:1000775 - yes Few but definitions not available ICD10CM:D57.09 D57.09 Hb-SS disease with crisis with other specified complication Sickle cell anemia with crisis with other specified complication D57.09 Hb-SS disease with crisis with other specified complication SCDO:1000783 When there is no deviation from the normal concentration of hemoglobin in the blood. None SCDO (Jade Hotchkiss) Normal Hemoglobin Concentration SCDO:1000784 A lack of production of hemoglobin S. Few but definitions not available SCDO (Jade Hotchkiss) MEDDRA:10055604 Absent Haemoglobin S Haemoglobin S Absent Hemoglobin S Absent Normal Haemoglobin S Level Normal Hemoglobin S Level Absent Hemoglobin S SCDO:1000786 - Few but definitions not freely available ICD10CM:D57.213 D57.213 Sickle Cell Disease-SC with cerebral vascular involvement Sickle-cell/Hb-C disease with cerebral vascular involvement D57.213 Sickle-cell/Hb-C disease with cerebral vascular involvement SCDO:1000787 - Few but definitions not freely available ICD10CM:D57.218 D57.218 Sickle Cell Disease-SC with crisis with other specified complication Sickle-cell/Hb-C disease with crisis with other specified complication D57.218 Sickle-cell/Hb-C disease with crisis with other specified complication SCDO:1000788 - Few but definitions not freely available ICD10CM:D57.413 D57.413 D57.413 Sickle-cell thalassemia, unspecified, with cerebral vascular involvement SCDO:1000789 - Few but definitions not freely available ICD10CM:D57.418 D57.418 Sickle-cell thalassemia, unspecified, with crisis with other specified complication D57.418 Sickle-cell thalassemia, unspecified, with crisis with other specified complication SCDO:1000790 - Few but definitions not freely available ICD10CM:D57.42 D57.42 Sickle-cell thalassemia beta zero without crisis D57.42 Sickle-cell thalassemia beta zero without crisis SCDO:1000791 - Few but definitions not freely available ICD10CM:D57.43 D57.43 Sickle-cell thalassemia beta zero with crisis D57.43 Sickle-cell thalassemia beta zero with crisis SCDO:1000792 - Few but definitions not freely available ICD10CM:D57.431 D57.431 Sickle-cell thalassemia beta zero with acute chest syndrome D57.431 Sickle-cell thalassemia beta zero with acute chest syndrome SCDO:1000793 - Few but definitions not freely available ICD10CM:D57.432 D57.432 Sickle-cell thalassemia beta zero with splenic sequestration D57.432 Sickle-cell thalassemia beta zero with splenic sequestration SCDO:1000794 - Few but definitions not freely available ICD10CM:D57.433 D57.433 Sickle-cell thalassemia beta zero with cerebral vascular involvement D57.433 Sickle-cell thalassemia beta zero with cerebral vascular involvement SCDO:1000795 - Few but definitions not freely available ICD10CM:D57.438 D57.438 Sickle-cell thalassemia beta zero with crisis with other specified complication D57.438 Sickle-cell thalassemia beta zero with crisis with other specified complication SCDO:1000796 - Few but definitions not freely available ICD10CM:D57.439 D57.439 Sickle-cell thalassemia beta zero with crisis, unspecified D57.439 Sickle-cell thalassemia beta zero with crisis, unspecified SCDO:1000797 - Few but definitions not freely available ICD10CM:D57.44 D57.44 Sickle-cell thalassemia beta minus without crisis Sickle-cell thalassemia beta plus without crisis D57.44 Sickle-cell thalassemia beta plus without crisis SCDO:1000798 - Few but definitions not freely available ICD10CM:D57.45 D57.45 Sickle-cell thalassemia beta minus with crisis Sickle-cell thalassemia beta plus with crisis D57.45 Sickle-cell thalassemia beta plus with crisis SCDO:1000799 - Few but definitions not freely available ICD10CM:D57.451 D57.451 Sickle-cell thalassemia beta minus with acute chest syndrome Sickle-cell thalassemia beta plus with acute chest syndrome D57.451 Sickle-cell thalassemia beta plus with acute chest syndrome SCDO:1000800 - Few but definitions not freely available ICD10CM:D57.452 D57.452 Sickle-cell thalassemia beta minus with splenic sequestration Sickle-cell thalassemia beta plus with splenic sequestration D57.452 Sickle-cell thalassemia beta plus with splenic sequestration SCDO:1000801 - Few but definitions not freely available ICD10CM:D57.453 D57.453 Sickle-cell thalassemia beta minus with cerebral vascular involvement Sickle-cell thalassemia beta plus with cerebral vascular involvement D57.453 Sickle-cell thalassemia beta plus with cerebral vascular involvement SCDO:1000802 - Few but definitions not freely available ICD10CM:D57.458 D57.458 Sickle-cell thalassemia beta minus with crisis with other specified complication Sickle-cell thalassemia beta plus with crisis with other specified complication D57.458 Sickle-cell thalassemia beta plus with crisis with other specified complication SCDO:1000803 - Few but definitions not freely available ICD10CM:D57.459 D57.459 Sickle-cell thalassemia beta minus with crisis, unspecified Sickle-cell thalassemia beta plus with crisis, unspecified D57.459 Sickle-cell thalassemia beta plus with crisis, unspecified SCDO:1000804 - Few but definitions not freely available ICD10CM:D57.818 D57.818 D57.818 Other sickle-cell disorders with crisis with other specified complication SCDO:1000805 - Few but definitions not freely available ICD10CM:D57.813 D57.813 D57.813 Other sickle-cell disorders with cerebral vascular involvement SCDO:1000806 A lack of production of hemoglobin C. None SCDO (Jade Hotchkiss) Absent Haemoglobin C Haemoglobin C Absent Hemoglobin C Absent Normal Haemoglobin C Level Normal Hemoglobin C Level Absent Hemoglobin C SCDO:1000807 An elevated concentration in the blood of carboxyhemoglobin, which is the form of hemoglobin where the heme group has formed a stable complex with carbon monoxide (CO). Few but definitions not available SCDO (Jade Hotchkiss) Carboxyhemoglobin Increased Raised Carboxyhemoglobin Increased Carboxyhemoglobin SCDO:1000808 An abnormal reduction in the amount of oxygen bound to hemoglobin in arterial blood expressed as a percentage of the maximal binding capacity. Few but definitions not available SCDO (Jade Hotchkiss) Arterial Oxygen Saturation Decreased Decreased Arterial HbO2 Decreased Arterial Oxyhemoglobin Saturation Decreased Arterial SaO2 Decreased Arterial Sats Decreased Oxygen Saturation of Arterial Blood Decreased Oxyhemoglobin/Total Hemoglobin Low Arterial Oxygen Saturation Decreased Arterial Oxygen Saturation SCDO:1000812 A phenotype of the body's metabolism or homeostasis that is not clinically abnormal. None SCDO (Jade Hotchkiss) Normal Metabolism/Homeostasis Phenotype SCDO:1000813 When the degree to which oxygen is bound to hemoglobin in arterial blood is in the normal range. Few but definitions not available SCDO (Jade Hotchkiss) Normal Arterial Blood Oxygen Saturation Normal Arterial Oxygen Saturation SCDO:1000814 When the level of carboxyhemoglobin detected in a sample of blood falls in the normal range for carboxyhemoglobin. Few but definitions not available SCDO (Jade Hotchkiss) Carboxyhemoglobin Normal Normal Carboxyhemoglobin Concentration Normal Carboxyhemoglobin Level SCDO:1000815 When the level of methemoglobin detected in a sample of blood falls in the normal range for methemoglobin. None SCDO (Jade Hotchkiss) MetHb Normal Normal MetHb Level Normal Methemoglobin Concentration Normal Methemoglobin Level SCDO:1000816 A lack of production of hemoglobin D-Punjab. None SCDO (Jade Hotchkiss) Absent Haemoglobin D-Punjab Haemoglobin D-Punjab Absent Hemoglobin D-Punjab Absent Normal Haemoglobin D-Punjab Level Normal Hemoglobin D-Punjab Level Absent Hemoglobin D-Punjab SCDO:1000817 A lack of production of hemoglobin G-Philadelphia. None SCDO (Jade Hotchkiss) Absent Haemoglobin G-Philadelphia Haemoglobin G-Philadelphia Absent Hemoglobin G-Philadelphia Absent Normal Haemoglobin G-Philadelphia Level Normal Hemoglobin G-Philadelphia Level Absent Hemoglobin G-Philadelphia SCDO:1000818 A lack of production of hemoglobin O-Arab. None SCDO (Jade Hotchkiss) Absent Haemoglobin O-Arab Haemoglobin O-Arab Absent Hemoglobin O-Arab Absent Normal Haemoglobin O-Arab Level Normal Hemoglobin O-Arab Level Absent Hemoglobin O-Arab SCDO:1000819 An abnormal reduction in the pressure exerted by oxygen dissolved in the blood. Few but definitions not available SCDO (Jade Hotchkiss) Arterial Oxygen Partial Pressure Decreased Decreased Oxygen Tension Decreased PO2 Decreased PaO2 Decreased Partial Pressure of Blood Oxygen PO2 Decreased Decreased Partial Pressure of Oxygen SCDO:1000820 The observable morphological and physiological characteristics of the human blood cells or the organs associated with the development and formation of blood cells that are manifested through development and lifespan. Few but definitions not specific enough Haematopoietic System Phenotype Haemopoietic System Phenotype Hemopoietic System Phenotype Hematopoietic System Phenotype SCDO:1000821 A phenotype of the body's hematopoietic system that is not clinically abnormal. None SCDO (Jade Hotchkiss) Normal Hematopoietic System Phenotype SCDO:1000822 When the number of red blood cells in a specified volume of blood falls in the normal range. Few but definitions not available SCDO (Jade Hotchkiss) Normal RBC Count RBC Count Normal Red Blood Cell Count Normal Normal Red Blood Cell Count SCDO:1000823 When the number of white blood cells in a specified volume of blood falls in the normal range. Few but definitions not available SCDO (Jade Hotchkiss) Normal WBC Count WBC Count Normal White Blood Cell Count Normal Normal White Blood Cell Count SCDO:1000824 When the number of platelets in a specified volume of blood falls in the normal range. Few but definitions not available SCDO (Jade Hotchkiss) Platelet Count Normal Normal Platelet Count SCDO:1000825 When the average volume or size of a single red blood cell falls in the normal range. Few but definitions not available SCDO (Jade Hotchkiss) MCV Normal Mean Cell Volume Normal Mean Corpuscular Volume Normal Normal MCV Normal Mean Cell Volume Normal Mean Corpuscular Volume SCDO:1000826 When the average amount of hemoglobin per red blood cell (calculated by dividing the total mass of hemoglobin by the number of red blood cells in a volume of blood) falls in the normal range. Few but definitions not available SCDO (Jade Hotchkiss) MCH Normal Mean Cell Hemoglobin Normal Mean Corpuscular Hemoglobin Level Normal Mean Corpuscular Hemoglobin Normal Normal MCH Normal Mean Cell Hemoglobin Normal Mean Corpuscular Hemoglobin Normal Mean Corpuscular Hemoglobin Level Normal Mean Corpuscular Hemoglobin SCDO:1000827 When the amount of hemoglobin in a given volume of packed red blood cells falls in the normal range. None SCDO (Jade Hotchkiss) MCHC Normal Mean Corpuscular Hemoglobin Concentration Normal Normal MCHC Normal Mean Cell Hemoglobin Concentration Normal Mean Corpuscular Hemoglobin Concentration SCDO:1000828 When the range of variation of red blood cell (RBC) volume falls in the normal range. Few but definitions not available SCDO (Jade Hotchkiss) Normal RBC Distribution Width Normal RCDW RBC Distribution Width Normal RCDW Normal Red Blood Cell Distribution Width Normal Normal Red Blood Cell Distribution Width SCDO:1000829 When the level of serum creatinine is in the normal range. Few but definitions not available SCDO (Jade Hotchkiss) Normal Serum Creatinine Level Serum Creatinine Level Normal Serum Creatinine Normal Normal Serum Creatinine SCDO:1000830 When the level of serum alanine aminotransferase is in the normal range. Few but definitions not available SCDO (Jade Hotchkiss) ALT Level Normal ALT Normal Normal ALT Normal ALT Level Normal Alanine Aminotransferase Level Normal Alanine Transaminase Normal Serum Alanine Aminotransferase Level Serum Alanine Aminotransferase Level Normal Serum Alanine Aminotransferase Normal Normal Serum Alanine Aminotransferase SCDO:1000831 When the level of serum aspartate aminotransferase is in the normal range. Few but definitions not available SCDO (Jade Hotchkiss) AST Level Normal AST Normal Normal AST Normal AST Level Normal Aspartate Aminotransferase Normal Serum AST Normal Serum Aspartate Aminotransferase Level Serum AST Normal Serum Aspartate Aminotransferase Normal Normal Serum Aspartate Aminotransferase SCDO:1000832 When the level of serum alkaline aminotransferase is in the normal range. Few but definitions not available SCDO (Jade Hotchkiss) AP Level Normal AP Normal Alkaline Phosphatase Level Normal Alkaline Phosphatase Normal Normal AP Normal AP Level Normal Serum AP Level Normal Serum Alkaline Phosphatase Level Normal Serum Alkaline Phosphatase SCDO:1000833 When the level of the enzyme lactate dehydrogenase in the serum is in the normal range. Few but definitions not available SCDO (Jade Hotchkiss) LD Level Normal LD Normal LDH Level Normal LDH Normal Lactate Dehydrogenase Level Normal Lactate Dehydrogenase Normal Normal LD Normal LD Level Normal LDH Normal LDH Level Normal Lactate Dehydrogenase Level SCDO:1000834 When the number of reticulocytes in a specified volume of blood falls in the normal range. Few but definitions not available SCDO (Jade Hotchkiss) Reticulocyte Count Normal Normal Reticulocyte Count SCDO:1000835 When the total bilirubin level in the serum is in the normal range. Few but definitions not available SCDO (Jade Hotchkiss) Serum Bilirubin Total Normal Total Serum Bilirubin Level Normal Total Serum Bilirubin Normal Normal Total Serum Bilirubin SCDO:1000836 When the concentration of urinary albumin falls in the normal range. None SCDO (Jade Hotchkiss) Normal Urinary Albumin Concentration Urinary Albumin Concentration Normal Urine Albumin Concentration Normal Normal Urine Albumin Concentration SCDO:1000837 When the concentration of urine creatinine falls in the normal range. Few but definitions not available SCDO (Jade Hotchkiss) Creatinine Urine Normal Normal Urinary Creatinine Normal Urinary Creatinine Level Normal Urine Creatinine Urinary Creatinine Level Normal Urine Creatinine Level Normal Normal Urine Creatinine Level SCDO:1000838 When the pressure exerted by oxygen dissolved in the blood falls in the normal range. None SCDO (Jade Hotchkiss) Normal Oxygen Tension Normal PO2 Normal PaO2 Normal Partial Pressure of Blood Oxygen PO2 Normal PaO2 Normal Partial Pressure of Blood Oxygen Normal Partial Pressure of Oxygen Normal Normal Partial Pressure of Oxygen SCDO:1000839 When the pressure exerted by carbon dioxide dissolved in the blood falls in the normal range. None SCDO (Jade Hotchkiss) Normal Carbon Dioxide Tension Normal PaCO2 Normal Partial Pressure of Blood Carbon Dioxide PaCO2 Normal Partial Pressure of Blood Carbon Dioxide Normal Partial Pressure of Carbon Dioxide Normal Normal Partial Pressure of Carbon Dioxide SCDO:1000840 An abnormal reduction in the pressure exerted by carbon dioxide dissolved in the blood. None SCDO (Jade Hotchkiss) Decreased PCO2 Decreased PaCO2 Decreased Partial Pressure of Blood Carbon Dioxide PCO2 Decreased PaCO2 Decreased Partial Pressure of Blood Carbon Dioxide Decreased Decreased Partial Pressure of Carbon Dioxide SCDO:1000841 An abnormal increase in the pressure exerted by carbon dioxide dissolved in the blood. None SCDO (Jade Hotchkiss) Elevated Partial Pressure of Carbon Dioxide Increased PCO2 Increased PaCO2 Increased Partial Pressure of Blood Carbon Dioxide PCO2 Increased PaCO2 Increased Partial Pressure of Carbon Dioxide Increased Raised Partial Pressure of Carbon Dioxide Increased Partial Pressure of Carbon Dioxide SCDO:1000842 Clinical manifestation consisting of a deficiency of carbon dioxide in arterial blood. Sufficient SCDO:1000842 MESH:D016857 Hypocarbia Hypocapnia SCDO:1000843 A clinical manifestation of abnormal increase in the amount of carbon dioxide in arterial blood. Sufficient SCDO:1000843 MESH:D006935 Hypercarbia Hypercapnia SCDO:1000844 When the abnormal hemoglobin, hemoglobin S (HbS), has been detected in a blood sample. None SCDO (Jade Hotchkiss) Haemoglobin S Present Haemoglobin S in Blood HbS Present HbS in Blood Hemoglobin S in Blood Hemoglobin S Present SCDO:1000847 The Sickle in Africa core data element that records the type of visit undertaken by a patient. 1, Routine 2, Acute 3, Review 4, First visit Type of visit visit_type Demographics 2 dropdown SickleInAfrica CDE - Type of Visit Question SCDO:1000849 A clinical visit occuring because of an acute (severe with sudden onset) health condition. Few but definitions not specific enough SCDO (Jade Hotchkiss) Acute Clinical Visit SCDO:1000850 The Sickle in Africa core data element that records the patient's medical record number. Medical record number (MRN) medical_record_number Demographics 4 text MRN Medical record number SickleInAfrica CDE - Medical Record Number Question SCDO:1000854 The Sickle in Africa core data element that records the name of the hospital that a patient visited. Hospital name hospital_name Demographics 5 text SickleInAfrica CDE - Hospital Name Question SCDO:1000855 The name of the hospital visited by a patient. None SCDO (Jade Hotchkiss) Hospital Name SCDO:1000856 The Sickle in Africa core data element that records a respondent's first name. First name first_name Demographics 6 text SickleInAfrica CDE - First Name Question SCDO:1000857 The Sickle in Africa core data element that records a respondent's middle name. Middle name middle_name Demographics 7 text SickleInAfrica CDE - Middle Name Question SCDO:1000858 A first name is a name that denotes a specific individual between members of a group of individuals, whose members usually share the same surname. Sufficient SCDO:1000858 sio:FirstName Forename Given Name First Name SCDO:1000860 A middle name is a name assigned to an individual that is not the first or last name. Sufficient SCDO:1000860 sio:MiddleName Middle Name SCDO:1000861 A last name (surname) is a name added to a given name and is part of a personal name and is often the family name. Sufficient SCDO:1000861 sio:LastName Last Name SCDO:1000862 The Sickle in Africa core data element that records a respondent's last name. Last name last_name Demographics 8 text SickleInAfrica CDE - Last Name Question SCDO:1000863 The Sickle in Africa core data element that records a respondent's height. Height/Length height_length Demographics cm 12 Number text SickleInAfrica CDE - Height Question SCDO:1000866 The Sickle in Africa core data element that records a respondent's measured weight. Weight weight Demographics kg 13 Number text SickleInAfrica CDE - Weight Question SCDO:1000868 The Sickle in Africa core data element that records the ethnic group to which a respondent belongs. Ethnic Group tribe Demographics 16 text SickleInAfrica CDE - Ethnic Group Question SCDO:1000869 The Sickle in Africa core data element that records the religion of a respondent. Religion religion Demographics 17 text SickleInAfrica CDE - Religion Question SCDO:1000870 The Sickle in Africa core data element that records the region in which the respondent lives. Region region Demographics 18 text SickleInAfrica CDE - Region Question SCDO:1000871 A street name is the token given to identify a particular street. Sufficient SCDO:1000871 SIO:000766 Street Name SCDO:1000872 The Sickle in Africa core data element that records the name of the street in which the respondent lives. Street street Demographics 19 text SickleInAfrica CDE - Street Question SCDO:1000873 The Sickle in Africa core data element that records the landmark that is nearest to where the participant lives. Nearest landmark nearest_landmark Demographics 20 text SickleInAfrica CDE - Nearest Landmark Question SCDO:1000874 A recognizable natural or artificial geographic feature, used for navigation (often visible from long distances), that is nearest to where the participant lives. None SCDO (Jade Hotchkiss) Nearest Geographical Landmark SCDO:1000875 The name of a respondent's next of kin. None SCDO (Jade Hotchkiss) Next of Kin Name SCDO:1000876 The Sickle in Africa core data element that records the participant's primary telephone number. Telephone 1 telephone_1 Demographics 21 text SickleInAfrica CDE - Telephone 1 Question SCDO:1000877 The Sickle in Africa core data element that records the participant's secondary telephone number. Telephone 2 telephone_2 Demographics 22 text SickleInAfrica CDE - Telephone 2 Question SCDO:1000878 The Sickle in Africa core data element that records the name of the participant's next of kin. Next of kin name next_of_kin_name Demographics 23 text SickleInAfrica CDE - Next of Kin Name Question SCDO:1000879 The Sickle in Africa core data element that records the telephone number of the participant's next of kin. Next of kin telephone number next_of_kin_telephone_numb Demographics 24 text SickleInAfrica CDE - Next of Kin Number Question SCDO:1000880 The Sickle in Africa core data element that records the participant's next of kin's relationship to the participant. Relationship to participant next_of_kin_relationship Demographics 25 text SickleInAfrica CDE - Relationship to Participant Question SCDO:1000882 A respondent's primary telephone number. None SCDO (Jade Hotchkiss) Telephone Number 1 SCDO:1000883 A respondent's secondary telephone number. None SCDO (Jade Hotchkiss) Telephone Number 2 SCDO:1000884 The telephone number of a respondent's next of kin. None SCDO (Jade Hotchkiss) Next of Kin Telephone Number SCDO:1000885 The relationship that the participant's next of kin has with the participant. None SCDO (Jade Hotchkiss) Next of Kin Relationship to Patient Next of Kin Relationship to Participant SCDO:1000886 The Sickle in Africa core data element that records whether the participant was given a blood transfusion. 1, Yes 0, No Blood transfusion blood_transfusion Management Details 7 yesno SCDO (Jade Hotchkiss) SickleInAfrica CDE - Blood Transfusion Question SCDO:1000887 The Sickle in Africa core data element that records the number of units of blood that a participant was given during a blood transfusion. Units transfused units_transfused Management Details 9 Number [blood_transfusion] = "Yes" text SickleInAfrica CDE - Units Transfused Question SCDO:1000888 The number of units of blood that a patient received during a blood transfusion. None SCDO (Jade Hotchkiss) Number of Units Transfused SCDO:1000889 The Sickle in Africa core data element that records whether a participant has difficulty in breathing. 1, Yes 0, No Difficulty in breathing difficulty_in_breathing Vital Signs 4 yesno SickleInAfrica CDE - Difficulty in Breathing Question SCDO:1000890 The Sickle in Africa core data element that records a participant's systolic blood pressure. Systolic blood pressure systolic_blood_press Vital Signs mmHg 5 text SickleInAfrica CDE - Systolic Blood Pressure Question SCDO:1000891 The Sickle in Africa core data element that records a participant's diastolic blood pressure. Diastolic blood pressure diastol_blood_press Vital Signs mmHg 6 text SickleInAfrica CDE - Diastolic Blood Pressure Question SCDO:1000894 The Sickle in Africa core data element that records whether a participant has priapism. 1, Yes 0, No Priapism priapism Vital Signs 7 yesno SickleInAfrica CDE - Priapism Question SCDO:1000895 The Sickle in Africa core data element that records whether a participant has chest pain. 1, Yes 0, No Chest Pain chest_pain Vital Signs 8 yesno SCDO (Jade Hotchkiss) SickleInAfrica CDE - Chest Pain Question SCDO:1000896 The Sickle in Africa core data element that records whether a participant has anaemia. 1, Yes 0, No Anaemia anaemia Vital Signs 9 yesno SCDO (Jade Hotchkiss) SickleInAfrica CDE - Anaemia Question SCDO:1000897 The Sickle in Africa core data element that records whether a participant has jaundice. 1, Yes 0, No Jaundice jaundice Vital Signs 10 yesno SickleInAfrica CDE - Jaundice Question SCDO:1000898 The Sickle in Africa core data element that collects the concentration of urea in the respondent's blood. Urea urea Kidney Function Assay (Phenx protocols PX141401, PX141501 and PX141601 unless stated otherwise) mmol/L 2 Number text SickleInAfrica CDE - Urea Question SCDO:1000900 A clinical visit that is the patient's first clinical visit. None SCDO (Jade Hotchkiss) First Visit SCDO:1000901 A clinical visit that is a follow-up for a previous visit. Not relevant to context of sickle cell SCDO (Jade Hotchkiss) Review Visit Follow-Up Visit STATO:0000091 Genome wide association study is a kind of study whose objective is to detect association between genetic markers (SNP or otherwise) accross the genome and a trait which may be a disease or another phenotype (e.g. trait of agronomic relevance in animal or plant studies). Genome wide association study compare the allele frequencies in 2 populations, one free of the trait used as control, the other one showing the trait use as 'case'. GWAS studies implement case-control design. http://purl.obolibrary.org/obo/STATO_0000091 Sufficient SCDO:0000450 STATO:0000091 GWAS Genome Wide Association Study SYMP:0000412 A neurological and physiological symptom characterized by a painful or apprehensive uneasiness of mind usually over an impending or anticipated ill. http://purl.obolibrary.org/obo/SYMP_0000412 Sufficient SCDO:0000068 http://www.apa.org/topics/anxiety/ SYMP:0000412 Anxiety Symptoms Panic Worry Physical symptoms include increased blood pressure (rapid heartbeat), trembling or dizziness. Anxiety SYMP:0019161 Muscle pain is a pain characterized by pain in one or more muscles. Provide source for additional info http://purl.obolibrary.org/obo/SYMP_0019161 Over-stretching of one muscle or a group of muscles, trauma, infections ( influenza, Lyme, Ebola, Dengue fever, Chicungunya fever, Babesiosis, Malaria, Toxoplasmosis, Hemorrhage fever, polio, Rocky Mountain spotted fever, Trichinosis), vaccines, muscle hematoma, autoimmune disorders ( lupus, polymyalgia, polymyositis, nutricional deficiencies, chronic fatigue syndrome, acute rejection after heart transplant surgery, rhabdomyolysis, severe potassium deficiency, fibromialgia, muscle abscess , reaction to drugs ( statins, fibrates, ACE inhibitors, cocaine), repetitive strain injury,withdrawal syndrome of certain drugs ( corticosteroids, opioids, barbiturates, benzodiazepines, caffeine, alcohol). Pain of a muscle or a group of muscles. Sufficient SCDO:0000779 SYMP:0019161 Myalgia Muscle Pain UO:0000000 A standardized quantity of a physical quality. Sufficient SCDO:1000478 UO:0000000 Unit Unit of Measure Units Unit of Measurement UO:0000001 A unit which is a standard measure of the distance between two points. Sufficient SCDO:1000864 UO:0000001 Length Unit UO:0000002 A unit which is a standard measure of the amount of matter/energy of a physical object. Sufficient SCDO:1000628 UO:0000002 Mass Unit UO:0000005 A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter. Sufficient SCDO:1000712 UO:0000005 Temperature Unit UO:0000009 A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France. Sufficient SCDO:1000867 UO:0000009 Kilogram UO:0000015 A length unit which is equal to one hundredth of a meter or 10^[-2] m. Sufficient SCDO:1000865 UO:0000015 Centimeter UO:0000025 A mass unit which is equal to 10^[-12] g. Sufficient SCDO:1000629 UO:0000025 picogram pg UO:0000051 A unit which represents a standard measurement of how much of a given substance there is mixed with another substance. Sufficient SCDO:1000491 UO:0000051 Concentration Unit UO:0000095 A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas. Sufficient SCDO:1000622 UO:0000095 Volume Unit UO:0000104 A volume unit which is equal to 10^[-15] L. Sufficient SCDO:1000623 UO:0000104 cubic micrometre femtoliter femtolitre μm^3 fL UO:0000109 A unit which is a standard measure of the force applied to a given area. Sufficient SCDO:1000720 UO:0000109 Pressure Unit UO:0000180 A concentration unit which is a standard measure of the mass of a substance in a given volume (density). Sufficient SCDO:1000506 UO:0000180 Unit of Density Definition from BioAssay Ontology Mass Per Unit Volume UO:0000186 A unit which is a standard measure of physical quantity consisting of only a numerical number without any units. Sufficient SCDO:1000642 UO:0000186 Dimensionless Unit UO:0000187 A dimensionless ratio unit which denotes numbers as fractions of 100. Sufficient SCDO:1000644 UO:0000187 % Percent UO:0000190 A dimensionless unit which denotes an amount or magnitude of one quantity relative to another. Sufficient SCDO:1000643 UO:0000190 Ratio UO:0000200 A concentration unit which denotes the average cell number in a given volume. Sufficient SCDO:1000503 UO:0000200 Cell Concentration Unit UO:0000272 A unit of pressure equal to the amount of fluid pressure one millimeter deep in mercury at zero degrees centigrade on Earth. Sufficient SCDO:1000721 UO:0000272 millimetres of mercury mmHg UO:0000280 A unit which represents a standard measurement occurrence of a process per unit time. Sufficient SCDO:1000715 UO:0000280 Rate Unit UO:0000316 A unit of cell concentration which is equal to one cell in a volume of 1 microliter. Sufficient SCDO:1000507 UO:0000316 cells per microliter cells/µL cells per microliter VO:0000001 A vaccine is a processed material with the function that when administered, it prevents or ameliorates a disorder in a target organism by inducing or modifying adaptive immune responses specific to the antigens in the vaccine. http://purl.obolibrary.org/obo/VO_0000001 Sufficient SCDO:0001221 VO:0000001 Vaccine VO:0000642 A viral vaccine that protects against infection with influenza virus. http://purl.obolibrary.org/obo/VO_0000642 Sufficient SCDO:0000642 VO:0000642 Influenza Virus Vaccine VO:0000675 A Streptococcal vaccine that is used against S. pneumoniae infection, which causes pneumococcal diseases. http://purl.obolibrary.org/obo/VO_0000675 Sufficient SCDO:0001109 VO:0000675 Pneumococcal Vaccine Streptococcus Pneumoniae Vaccine VT:0000202 The amount of alkaline phosphatase present in a specified volume of blood. The proportion, quantity, or volume in whole blood, serum, or plasma of this enzyme, which hydrolyzes orthophosphoric monoesters. Sufficient SCDO:1000499 VT:0000202 AP Level Blood Alkaline Phosphatase Amount Circulating ALP Level Circulating Alkaline Phosphatase Level Alkaline Phosphatase Level owl:Thing ERO:0001964 NCIT:C84981 NCIT:C84982 A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition. RO:0003302 causes or contributes to condition A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition. RO:0003303 results_in causes condition A relationship between a condition (phenotype or disease) and a relevant ICD-10-CM Diagnosis Code. None SCDO (Jade Hotchkiss) has clinical code A relation between a device (diagnostic device) and the recording of the output (diagnostic measurement) of the device. SCDO (Jade Hotchkiss) has output measurement A relation between a phenotype that is a diagnosis and a diagnostic tool used in making the diagnosis. SCDO (Jade Hotchkiss) diagnosed using tool A relation between a condition (phenotype or disease) and a type of treatment or a specific treatment, where the condition can be treated with the treatment. If required later, specify as inverse of "treats". SCDO (Jade Hotchkiss) treated with A measure that is critical to the collection of the measure at hand or is necessary for the interpretation of results for the measure at hand. Without such information, the data collected would be incomplete or misleading. SCDO (Jade Hotchkiss) Essential measures have been attributed according to information in PhenX. has essential measure A relation between a particular genotype or disorder and the pattern in which the particular genotype or disorder is passed from one generation to the next. SCDO (Jade Hotchkiss) has mode of inheritance A relationship between a condition (phenotype or disease), entity (aspect of quality of life) or process (therapy) and a disease modifier, where the condition, entity or process is modified by the disease modifier in some way. SCDO (Jade Hotchkiss) modified by A relationship between a disease modifier and a condition (phenotype or disease), entity (aspect of quality of life) or process (therapy), where the disease modifier modifies the condition, entity or process in some way. SCDO (Jade Hotchkiss) modifies A relation between a type of treatment or a specific treatment and a condition (phenotype or disease), where the type of treatment or specific treatment treat the condition. If required later, specify as inverse of "treated with". SCDO (Jade Hotchkiss) treats A relation between a condition (hemoglobinopathy) and the genotype that causes the condition. SCDO (Jade Hotchkiss) has causal genotype A relationship between an entity (e.g. genetic variation such as mutation or specific allele) and a genotype, where the entity contributes to the genotype. SCDO (Jade Hotchkiss) contributes to genotype A relationship between a diagnostic measurement and the diagnostic tool used to produce the measurement. SCDO (Jade Hotchkiss) obtained via diagnostic tool A relationship between a diagnostic device and the diagnostic tool by which the device is used. SCDO (Jade Hotchkiss) used by diagnostic tool A relation between a diagnostic tool (test, method, assay, etc.) and a diagnostic device, where the diagnostic device is used in the application of the diagnostic tool. SCDO (Jade Hotchkiss) uses diagnostic device A relation between a diagnostic measurement and a diagnostic device, where the diagnostic measurement is the output of the diagnostic device. SCDO (Jade Hotchkiss) output of diagnostic device A relation between a diagnostic tool and the diagnostic measurement that it measures. SCDO (Jade Hotchkiss) measures A relation between a genotype and a genetic variation (e.g. mutation or genetic recombination), where the genetic variation contributes to the genotype. SCDO (Jade Hotchkiss) has contributing genetic variation A condition (phenotype or disease) or event (adverse event) induced by an entity (e.g. a drug) or activity (e.g. exercise). The "developmentally induced by" object property in RO has the alternative term "induced by". SCDO (Jade Hotchkiss) induced by A relationship between a condition (a phenotype or disease) and an entity (e.g. environment) or condition (phenotype or disease) which could be an existing condition or an event, where the entity or second condition has a causal role for the condition being described. SCDO (Jade Hotchkiss) caused by A relation between a condition (disease or phenotype) or an entity (molecular phenotype) and a genetic variation (e.g. mutation or genetic recombination), where the genetic variation has some causal or contributing role that influences the condition or entity. SCDO (Jade Hotchkiss) has causal or contributing genetic variation A relation between an entity (genotype) and a molecular phenotype, where the entity has some causal or contributing role that influences the molecular phenotype. SCDO (Jade Hotchkiss) causes or contributes to molecular phenotype A relationship that holds between a condition such as a disease (hemoglobinopathy) and a phenotype (i.e. manifestation), where the phenotype is evidence of the condition. SCDO (Jade Hotchkiss) has manifestation A relation between a condition that is a diagnosis and a phenotype used in making the diagnosis. diagnosed by A relation between an Abnormal Phenotype that is a diagnosis and a Diagnostic Measurement or Diagnostic Device Visual Output used in making the diagnosis. SCDO (Jade Hotchkiss) diagnosed using measurement A relation between a genotype and a molecular phenotype, where the genotype has a causal role for the molecular phenotype. SCDO (Jade Hotchkiss) causes molecular phenotype A relation between a condition (disease such as a Hemoglobinopathy) and a molecular phenotype, where the molecular phenotype is evidence of the condition. SCDO (Jade Hotchkiss) has causal molecular phenotype A relationship between a Clinical or Research Assessment Data Element and a Clinical or Research Assessment Question Type. None SCDO (Jade Hotchkiss) is question type A relationship between a multiple choice data element and an answer option or a group of answer options that are provided to the respondent by the data element. None SCDO (Jade Hotchkiss) has answer option A relationship between a data element and the type of information that is collected by that data element. None SCDO (Jade Hotchkiss) collects A relationship between a data element and the unit of measurement used, as a standard, for the information that is collected by the data element. None SCDO (Jade Hotchkiss) has answer standard unit A relationship between a Diagnostic Measurement and a Phenotype, where the Phenotype is a possible finding of the Diagnostic Measurement, depending on the value recorded for the Diagnostic Measurement. SCDO (Jade Hotchkiss) has possible finding A relationship between a clinical code (such as ICD10 code) and a Phenotype, where the code can only be applied in instances where the phenotype is present. SCDO (Jade Hotchkiss) code requires phenotype A relation between an entity (phenotypic, therapeutic or diagnostic concept) and a guideline or directive. SCDO (Jade Hotchkiss) in guideline Sickle cell disease (SCD) is one of the most common monogenic diseases in humans with multiple phenotypic expressions that can manifest as both acute and chronic complications. Although described more than a century ago, challenges in comprehensive disease management and collaborative research on this disease are compounded by the complex molecular and clinical phenotypes of SCD, environmental and psychosocial factors, limited therapeutic options and ambiguous terminology. This ambiguous terminology has hampered the integration and interoperability of existing SCD knowledge, and SCD research translation. The SCD Ontology (SCDO), which is a community-driven integrative and universal knowledge representation system for SCD, overcomes this issue by providing a controlled vocabulary developed by a group of experts in both SCD and ontology design. SCDO is the first and most comprehensive standardized human- and machine-readable resource that unambiguously represents terminology and concepts about SCD for researchers, patients and clinicians. It is built around the central concept ‘hemoglobinopathy’, allowing inclusion of non-SCD haemoglobinopathies, such as thalassaemias, which may interfere with or influence SCD phenotypic manifestations. This collaboratively developed ontology constitutes a comprehensive knowledge management system and standardized terminology of various SCD-related factors. The SCDO will promote interoperability of different research datasets, facilitate seamless data sharing and collaborations, including meta-analyses within the SCD community, and support the development and curation of data-basing and clinical informatics in SCD. Anyone can access the resource. Manually, based on terms in existing ontologies and in collaboration with sickle cell disease (SCD) experts where necessary. As necessary. Not currently following a fixed frequency. Terms/classes are added as they are identified as necessary by the sickle cell disease (SCD) community. Researchers in Hemoglobinopathy and/or sickle cell disease (SCD), SCD patients and clinicians. First draft was made available in BioPortal in May 2017 OBO Foundry standards. The field of sickle cell disease (SCD) research and care. April 2021 English GPL-3.0 Visit your GP if you or your child have unexplained symptomssuch as balance and co-ordination problems or difficulty walking, talking or swallowing. Family and medical history: Your GP may ask whether you have any family history of ataxia. They will also want to know about the progression of your symptoms. They might carry out a simple assessment of your balance, walking and co-ordination. Your GP may also ask how much alcohol you drink and whether you're taking any form of medication. This is because excessive drinking and certain medications can cause ataxia-like symptoms in some people. You may be referred for a series of tests to rule out other possible causes of your symptoms, such as an infection. The tests will probably include blood and urine tests. Further testing: If your symptoms suggest you may have acquired ataxia because of a serious underlying condition, it's likely you'll be admitted immediately to your nearest hospital. Otherwise, you'll be referred to a neurologist (a specialist in brain and nervous system conditions) for further testing or, in the case of children, a paediatrician. Some of the tests you may have are described below. Genetic testing: Genetic testing involves taking a sample of blood and testing the DNA in it for any genetic mutation known to cause ataxia.Currently, tests can detect the mutations responsible for Friedreich's ataxia, ataxia-telangiectasia and most of the spinocerebellar ataxias. Brain scans: Brain scans can be used to check for physical abnormalities in the brain that could be caused by certain types of hereditary ataxia. They can also be used to check for other problems that may affect your brain, such as a brain tumour. The two most widely used brain imaging scans are: magnetic resonance imaging (MRI) scan – this uses a strong magnetic field and radio waves to produce detailed scans of the soft tissue of the brain. computerised tomography (CT) scan – where a series of X-raysare taken and assembled by a computer into a detailed three-dimensional image of your brain Other tests: Some of the other tests you may have to help diagnose ataxia and determine how severe it is can include: a lumbar puncture – where a sample of cerebrospinal fluid is taken from the base of the spine to check it for infection and any other abnormalities. nerve conduction studies and electromyography (EMG) – tests used to assess the electrical activity in nerves and muscles. videofluoroscopy – a continuous moving X-ray taken while you swallow different types of food and drink. an electrocardiogram (ECG) – an assessment of the electrical activity of the heart. an echocardiogram – an ultrasound scan of the heart. Surgery main treatments are lifestyle changes to ensure you remain as healthy as possible medication to control associated problems such as high blood pressure and high cholesterol dialysis – treatment to replicate some of the kidney's functions; this may be necessary in advanced CKD kidney transplant – this may also be necessary in advanced CKD Cancer can be caused by genetic factors; lifestyle factors such as tobacco use, diet, and physical activity; certain types of infections; and environmental exposures to different types of chemicals and radiation. Severely Increased Albuminuria Pulse Oximeter The production of an image obtained by cameras that detect the radioactive emissions of an injected radionuclide as it has distributed differentially throughout tissues in the body. The image obtained from a moving detector is called a scan, while the image obtained from a stationary camera device is called a scintiphotograph. no D011877 Scintigraphy May be Acute (acute kidney injury) or chronic (see chronic kidney disease). Hair-pulling Ddiagnosed by kidney biopsy - Diagnostic features include capillary wall thickening, normal cellularity, IgG and C3 along capillary walls on immunofluorescence, and subepithelial deposits on electron microscopy [KDIGO 2012]. Main treatments are lifestyle changes to ensure you remain as healthy as possible medication to control associated problems such as high blood pressure and high cholesterol dialysis – treatment to replicate some of the kidney's functions; this may be necessary in advanced CKD kidney transplant – this may also be necessary in advanced CKD main treatments are: lifestyle changes to ensure you remain as healthy as possible medication to control associated problems such as high blood pressure and high cholesterol dialysis – treatment to replicate some of the kidney's functions; this may be necessary in advanced CKD kidney transplant – this may also be necessary in advanced CKD Hemoglobin M Disease Pain Management Biologic therapy, Antibody therapy, Stem-cell transplantation, Splenectomy, Steroid treatment, Radioimmunotherapy, Surgery, chemotherapy, and radiation therapy, A list of essential measures, measures that are critical to the collection of the measure at hand or are necessary for the interpretation of results for the measure at hand. Without such information, the data collected would be incomplete or misleading. example to be eventually removed essential measures (annotations) Anti-inflammatory medications for joint pain and stiffness. Steroid creams for rashes. Corticosteroids to minimize the immune response. Antimalarial drugs for skin and joint problems. Test for Stroke Risk in Children with Sickle Cell Disease - TCD A measurement performed during physical examination to determine the size of the liver and identify possible hepatomegaly. yes uncurated Assessment for Hepatomegaly Test for Stroke Risk in Children with Sickle Cell Disease - TCDi Peritonitis, intraabdominal abscess, or sepsis, necrotizing myometritis, necrotizing fasciitis of the abdominal wall, septic pelvic thrombophlebitis, and toxic shock syndrome are rare complications, death. Amy be associated to secondary infertility. Visit your GP if you or your child have unexplained symptomssuch as balance and co-ordination problems or difficulty walking, talking or swallowing. Family and medical history: Your GP may ask whether you have any family history of ataxia. They will also want to know about the progression of your symptoms. They might carry out a simple assessment of your balance, walking and co-ordination. Your GP may also ask how much alcohol you drink and whether you're taking any form of medication. This is because excessive drinking and certain medications can cause ataxia-like symptoms in some people. You may be referred for a series of tests to rule out other possible causes of your symptoms, such as an infection. The tests will probably include blood and urine tests. Further testing: If your symptoms suggest you may have acquired ataxia because of a serious underlying condition, it's likely you'll be admitted immediately to your nearest hospital. Otherwise, you'll be referred to a neurologist (a specialist in brain and nervous system conditions) for further testing or, in the case of children, a paediatrician. Some of the tests you may have are described below. Genetic testing: Genetic testing involves taking a sample of blood and testing the DNA in it for any genetic mutation known to cause ataxia. Currently, tests can detect the mutations responsible for Friedreich's ataxia, ataxia-telangiectasia and most of the spinocerebellar ataxias. Brain scans: Brain scans can be used to check for physical abnormalities in the brain that could be caused by certain types of hereditary ataxia. They can also be used to check for other problems that may affect your brain, such as a brain tumour. The two most widely used brain imaging scans are: magnetic resonance imaging (MRI) scan – this uses a strong magnetic field and radio waves to produce detailed scans of the soft tissue of the brain. computerised tomography (CT) scan – where a series of X-raysare taken and assembled by a computer into a detailed three-dimensional image of your brain Other tests: Some of the other tests you may have to help diagnose ataxia and determine how severe it is can include: a lumbar puncture – where a sample of cerebrospinal fluid is taken from the base of the spine to check it for infection and any other abnormalities. nerve conduction studies and electromyography (EMG) – tests used to assess the electrical activity in nerves and muscles. videofluoroscopy – a continuous moving X-ray taken while you swallow different types of food and drink. an electrocardiogram (ECG) – an assessment of the electrical activity of the heart. an echocardiogram – an ultrasound scan of the heart. The branch of medicine that deals with the anatomy, functions and disorders of the nervous system. no Neurological disorders Neurology Blood tests, such as antibody tests and a complete blood count, a urinalysis and a chest X-ray. PMID:22655528 PMID:6690472